Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xdl Working: n-1-16.cluster.ucsf.bkslab.org:/scratch/xiaobo/170854/xdl-8058088.90 Result: /scratch/xiaobo/170854/xdl-8058088.90 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xdl 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/xdl mkdir: created directory `/scratch/xiaobo/170854' mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90' /scratch/xiaobo/170854/xdl-8058088.90 /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/170854/xdl-8058088.90/working' mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/protonate' Storing results in /scratch/xiaobo/170854/xdl-8058088.90/finished Working in /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 /scratch/xiaobo/170854/xdl-8058088.90/working/protonate /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Using inputs as protomers/tautomers. No processing done 460 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/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Bulk generating 3D conformations all protomers in /scratch/xiaobo/170854/xdl-8058088.90/working/3D mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/170854/xdl-8058088.90/working/protonate/xdl-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 ZINC000360805863 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building' mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360805863' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360805863 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000360805863 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360805863/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360805863 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/1 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](CCSC)NC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000360805863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360805863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360805863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000360805863 none CNC(=O)[C@H](CCSC)NC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', '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, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 9, 20, 3, 9, 9, 19, 21, 43, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 20, 20, 21, 21, 21, 21, 43, 43, 43, 3, 4, 4, 4, 4, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360805863 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000360805863 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/finished' Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360805863/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360805863 Building ZINC000431717262 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431717262 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/2 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1) `ZINC000431717262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431717262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000431717262 none COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 22, 22, 22, 22, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 33, 33, 33, 22, 22, 14, 14, 2, 6, 6, 6, 6, 6, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/3 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1) `ZINC000431717262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431717262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000431717262 none COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 22, 22, 22, 22, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 33, 33, 33, 22, 22, 14, 14, 2, 6, 6, 6, 6, 6, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000431717262 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 Building ZINC000431717262 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000431717262 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 2) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1) `ZINC000431717262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000431717262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000431717262 none COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 22, 22, 22, 22, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 33, 33, 33, 22, 22, 14, 14, 2, 6, 6, 6, 6, 6, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 3) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1) `ZINC000431717262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000431717262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000431717262 none COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 22, 22, 22, 22, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 33, 33, 33, 22, 22, 14, 14, 2, 6, 6, 6, 6, 6, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000431717262 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000431717262 Building ZINC000644081617 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644081617 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/4 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000644081617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644081617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000644081617 none CC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 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, 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] 0 hydrogens 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, 27, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 27, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27] 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]) total number of confs: 124 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/5 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000644081617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644081617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000644081617 none CC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 12, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 24, 30, 30, 30, 30, 30, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24] 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]) total number of confs: 110 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644081617 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 Building ZINC000644081617 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644081617 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 4) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000644081617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644081617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000644081617 none CC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 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, 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] 0 hydrogens 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, 27, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 27, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27] 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]) total number of confs: 124 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 5) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000644081617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644081617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000644081617 none CC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 12, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 24, 30, 30, 30, 30, 30, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24] 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]) total number of confs: 110 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644081617 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081617 Building ZINC000644081618 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644081618 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/6 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000644081618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644081618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000644081618 none CC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 27, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27] 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]) total number of confs: 120 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/7 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000644081618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644081618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000644081618 none CC[C@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 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, 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] 0 hydrogens 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, 26, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 26, 26, 26, 26, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 122 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644081618 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 Building ZINC000644081618 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644081618 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 6) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000644081618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644081618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000644081618 none CC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 27, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27] 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]) total number of confs: 120 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 7) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000644081618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644081618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000644081618 none CC[C@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 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, 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] 0 hydrogens 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, 26, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 26, 26, 26, 26, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 122 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644081618 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644081618 Building ZINC000360850200 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360850200 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/8 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CO)[C@H](C)C2)cn1) `ZINC000360850200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360850200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000360850200 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CO)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 5, 5, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 18, 8, 8, 8, 8, 5, 5, 20, 20, 20, 20, 20, 5, 8, 8, 18, 18, 54, 8, 8, 8, 8, 8, 5] 150 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/9 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CO)[C@H](C)C2)cn1) `ZINC000360850200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360850200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000360850200 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CO)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 18, 9, 9, 9, 9, 5, 5, 18, 18, 18, 18, 18, 5, 9, 9, 18, 18, 54, 9, 9, 9, 9, 9, 5] 150 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]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000360850200 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 Building ZINC000360850200 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360850200 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 8) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CO)[C@H](C)C2)cn1) `ZINC000360850200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360850200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000360850200 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CO)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 5, 5, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 18, 8, 8, 8, 8, 5, 5, 20, 20, 20, 20, 20, 5, 8, 8, 18, 18, 54, 8, 8, 8, 8, 8, 5] 150 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 9) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CO)[C@H](C)C2)cn1) `ZINC000360850200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360850200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000360850200 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CO)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 18, 9, 9, 9, 9, 5, 5, 18, 18, 18, 18, 18, 5, 9, 9, 18, 18, 54, 9, 9, 9, 9, 9, 5] 150 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]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000360850200 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850200 Building ZINC000360850201 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360850201 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/10 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)[C@H](CO)C2)cn1) `ZINC000360850201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360850201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000360850201 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)[C@H](CO)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 4, 4, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 10, 10, 20, 10, 4, 4, 16, 16, 16, 16, 16, 4, 10, 10, 10, 10, 10, 20, 20, 60, 10, 10, 4] 150 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]) total number of confs: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/11 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)[C@H](CO)C2)cn1) `ZINC000360850201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360850201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000360850201 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)[C@H](CO)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 9, 9, 15, 9, 5, 5, 18, 18, 18, 18, 18, 5, 9, 9, 9, 9, 9, 15, 15, 45, 9, 9, 5] 150 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000360850201 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 Building ZINC000360850201 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360850201 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 10) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)[C@H](CO)C2)cn1) `ZINC000360850201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360850201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000360850201 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)[C@H](CO)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 4, 4, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 10, 10, 20, 10, 4, 4, 16, 16, 16, 16, 16, 4, 10, 10, 10, 10, 10, 20, 20, 60, 10, 10, 4] 150 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]) total number of confs: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 11) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)[C@H](CO)C2)cn1) `ZINC000360850201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360850201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000360850201 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)[C@H](CO)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 9, 9, 15, 9, 5, 5, 18, 18, 18, 18, 18, 5, 9, 9, 9, 9, 9, 15, 15, 45, 9, 9, 5] 150 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000360850201 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000360850201 Building ZINC001754765309 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001754765309 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/12 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 21, 21, 21, 21, 38, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 63, 21, 21, 33, 33, 50, 50, 50, 50, 50, 50, 50, 21, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 245 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/13 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 23, 23, 23, 23, 37, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 69, 23, 23, 35, 35, 50, 50, 50, 50, 50, 50, 50, 23, 23] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 267 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/14 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/14' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 18, 18, 18, 18, 36, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 54, 18, 18, 34, 34, 50, 50, 50, 50, 50, 50, 50, 18, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/15 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/15' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 23, 23, 23, 23, 38, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 69, 23, 23, 36, 36, 50, 50, 50, 50, 50, 50, 50, 23, 23] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001754765309 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 Building ZINC001754765309 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001754765309 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 12) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 21, 21, 21, 21, 38, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 63, 21, 21, 33, 33, 50, 50, 50, 50, 50, 50, 50, 21, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 245 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 13) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 23, 23, 23, 23, 37, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 69, 23, 23, 35, 35, 50, 50, 50, 50, 50, 50, 50, 23, 23] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 267 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 14) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 18, 18, 18, 18, 36, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 54, 18, 18, 34, 34, 50, 50, 50, 50, 50, 50, 50, 18, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 15) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 23, 23, 23, 23, 38, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 69, 23, 23, 36, 36, 50, 50, 50, 50, 50, 50, 50, 23, 23] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001754765309 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 Building ZINC001754765309 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001754765309 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 12) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 21, 21, 21, 21, 38, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 63, 21, 21, 33, 33, 50, 50, 50, 50, 50, 50, 50, 21, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 245 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 13) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 23, 23, 23, 23, 37, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 69, 23, 23, 35, 35, 50, 50, 50, 50, 50, 50, 50, 23, 23] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 267 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 14) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 18, 18, 18, 18, 36, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 54, 18, 18, 34, 34, 50, 50, 50, 50, 50, 50, 50, 18, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 15) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 23, 23, 23, 23, 38, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 69, 23, 23, 36, 36, 50, 50, 50, 50, 50, 50, 50, 23, 23] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001754765309 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 Building ZINC001754765309 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001754765309 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 12) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 21, 21, 21, 21, 38, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 63, 21, 21, 33, 33, 50, 50, 50, 50, 50, 50, 50, 21, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 245 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 13) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 23, 23, 23, 23, 37, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 69, 23, 23, 35, 35, 50, 50, 50, 50, 50, 50, 50, 23, 23] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 267 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 14) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 18, 18, 18, 18, 36, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 54, 18, 18, 34, 34, 50, 50, 50, 50, 50, 50, 50, 18, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 15) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1) `ZINC001754765309.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001754765309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001754765309 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(O)C[N@](CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 23, 23, 23, 23, 38, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 69, 23, 23, 36, 36, 50, 50, 50, 50, 50, 50, 50, 23, 23] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001754765309 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754765309 Building ZINC000158102401 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000158102401 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/16 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000158102401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000158102401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000158102401 none CCCNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 7, 4, 7, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 12, 4, 27, 27, 27, 27, 27, 20, 20, 7, 4, 4, 4, 4, 2, 4, 12, 12, 12, 12, 12, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/17 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000158102401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000158102401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000158102401 none CCCNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 7, 4, 7, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 14, 5, 27, 27, 27, 27, 27, 21, 21, 7, 4, 4, 4, 4, 2, 5, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000158102401 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 Building ZINC000158102401 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000158102401 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 16) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000158102401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000158102401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000158102401 none CCCNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 7, 4, 7, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 12, 4, 27, 27, 27, 27, 27, 20, 20, 7, 4, 4, 4, 4, 2, 4, 12, 12, 12, 12, 12, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 17) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000158102401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000158102401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000158102401 none CCCNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 7, 4, 7, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 14, 5, 27, 27, 27, 27, 27, 21, 21, 7, 4, 4, 4, 4, 2, 5, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000158102401 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000158102401 Building ZINC001754811280 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001754811280 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/18 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1C) `ZINC001754811280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001754811280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001754811280 none COCCNC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 24, 15, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 40, 40, 24, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/19 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1C) `ZINC001754811280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001754811280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001754811280 none COCCNC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 26, 16, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 38, 38, 26, 16, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001754811280 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 Building ZINC001754811280 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001754811280 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 18) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COCCNC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1C) `ZINC001754811280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001754811280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001754811280 none COCCNC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 24, 15, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 40, 40, 24, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 19) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COCCNC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1C) `ZINC001754811280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001754811280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001754811280 none COCCNC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 26, 16, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 38, 38, 26, 16, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001754811280 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001754811280 Building ZINC000685879103 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000685879103 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/20 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(CC(N)=O)cc1) `ZINC000685879103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000685879103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000685879103 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(CC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 11, 11, 42, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 42, 42, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/21 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(CC(N)=O)cc1) `ZINC000685879103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000685879103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000685879103 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(CC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 21, 21, 17, 21, 41, 50, 50, 21, 21, 1, 1, 1, 1, 1, 1, 2, 11, 11, 21, 21, 41, 41, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000685879103 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 Building ZINC000685879103 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000685879103 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 20) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(CC(N)=O)cc1) `ZINC000685879103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000685879103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000685879103 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(CC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 11, 11, 42, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 42, 42, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 21) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(CC(N)=O)cc1) `ZINC000685879103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000685879103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000685879103 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(CC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 21, 21, 17, 21, 41, 50, 50, 21, 21, 1, 1, 1, 1, 1, 1, 2, 11, 11, 21, 21, 41, 41, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000685879103 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685879103 Building ZINC000174248617 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174248617 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/22 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCNC(C)(C)C)cn1) `ZINC000174248617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174248617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000174248617 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCNC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 16, 20, 29, 30, 30, 30, 8, 8, 8, 8, 8, 8, 3, 16, 16, 20, 20, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/23 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCNC(C)(C)C)cn1) `ZINC000174248617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174248617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000174248617 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCNC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 16, 22, 30, 30, 30, 30, 7, 7, 7, 7, 7, 7, 4, 16, 16, 22, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000174248617 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 Building ZINC000174248617 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174248617 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 22) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCNC(C)(C)C)cn1) `ZINC000174248617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174248617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000174248617 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCNC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 16, 20, 29, 30, 30, 30, 8, 8, 8, 8, 8, 8, 3, 16, 16, 20, 20, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 23) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCNC(C)(C)C)cn1) `ZINC000174248617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174248617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000174248617 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCNC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 16, 22, 30, 30, 30, 30, 7, 7, 7, 7, 7, 7, 4, 16, 16, 22, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000174248617 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174248617 Building ZINC000174906427 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174906427 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/24 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3ccncc32)cn1) `ZINC000174906427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174906427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000174906427 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3ccncc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 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: [12, 12, 12, 1, 1, 1, 3, 14, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 12] 45 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/25 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3ccncc32)cn1) `ZINC000174906427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174906427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000174906427 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3ccncc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 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: [11, 11, 11, 1, 1, 1, 3, 14, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 11] 45 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000174906427 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 Building ZINC000174906427 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174906427 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 24) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3ccncc32)cn1) `ZINC000174906427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174906427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000174906427 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3ccncc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 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: [12, 12, 12, 1, 1, 1, 3, 14, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 12] 45 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 25) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3ccncc32)cn1) `ZINC000174906427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174906427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000174906427 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3ccncc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 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: [11, 11, 11, 1, 1, 1, 3, 14, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 11] 45 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000174906427 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174906427 Building ZINC000170718286 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000170718286 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/26 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3ccnn3)cc2)cn1) `ZINC000170718286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000170718286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000170718286 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3ccnn3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 19, 19, 12, 19, 38, 38, 38, 38, 19, 19, 12, 12, 12, 12, 12, 12, 6, 19, 19, 38, 38, 19, 19, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/27 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3ccnn3)cc2)cn1) `ZINC000170718286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000170718286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000170718286 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3ccnn3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 18, 18, 11, 18, 37, 37, 37, 37, 18, 18, 12, 12, 12, 12, 12, 12, 6, 18, 18, 37, 37, 18, 18, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000170718286 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 Building ZINC000170718286 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000170718286 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 26) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3ccnn3)cc2)cn1) `ZINC000170718286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000170718286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000170718286 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3ccnn3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 19, 19, 12, 19, 38, 38, 38, 38, 19, 19, 12, 12, 12, 12, 12, 12, 6, 19, 19, 38, 38, 19, 19, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 27) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3ccnn3)cc2)cn1) `ZINC000170718286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000170718286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000170718286 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3ccnn3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 18, 18, 11, 18, 37, 37, 37, 37, 18, 18, 12, 12, 12, 12, 12, 12, 6, 18, 18, 37, 37, 18, 18, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000170718286 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170718286 Building ZINC000685894649 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000685894649 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/28 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1cn[nH]c1) `ZINC000685894649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000685894649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000685894649 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1cn[nH]c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 5, 5, 5, 23, 37, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 37, 37, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/29 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1cn[nH]c1) `ZINC000685894649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000685894649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000685894649 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1cn[nH]c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 26, 38, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 6, 26, 26, 38, 38, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000685894649 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 Building ZINC000685894649 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000685894649 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 28) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1cn[nH]c1) `ZINC000685894649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000685894649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000685894649 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1cn[nH]c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 5, 5, 5, 23, 37, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 37, 37, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 29) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1cn[nH]c1) `ZINC000685894649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000685894649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000685894649 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1cn[nH]c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 26, 38, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 6, 26, 26, 38, 38, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000685894649 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000685894649 Building ZINC000175319747 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175319747 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/30 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)sc1C) `ZINC000175319747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175319747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000175319747 none Cc1nc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 14, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35, 12, 12, 2, 5, 5, 5, 5, 5, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/31 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)sc1C) `ZINC000175319747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175319747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000175319747 none Cc1nc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 14, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35, 12, 12, 2, 5, 5, 5, 5, 5, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000175319747 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 Building ZINC000175319747 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175319747 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 30) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)sc1C) `ZINC000175319747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175319747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000175319747 none Cc1nc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 14, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35, 12, 12, 2, 5, 5, 5, 5, 5, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 31) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)sc1C) `ZINC000175319747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175319747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000175319747 none Cc1nc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 14, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35, 12, 12, 2, 5, 5, 5, 5, 5, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000175319747 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175319747 Building ZINC000170852404 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000170852404 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/32 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnn[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000170852404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000170852404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC000170852404 none O=C(Nc1nnn[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 8, 8, 6, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 8, 10, 11, 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, 9, 9, 9, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 9, 5, 5, 5, 5] 10 rigid atoms, others: [1, 10, 11, 9] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/33 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnn[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000170852404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000170852404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC000170852404 none O=C(Nc1nnn[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 8, 8, 6, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 8, 10, 11, 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, 9, 9, 9, 9, 9, 1, 1, 1, 5, 5, 1, 1, 5, 5, 9, 5, 5, 5, 5] 10 rigid atoms, others: [1, 9, 10, 11] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000170852404 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 Building ZINC000170852404 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000170852404 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 32) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(Nc1nnn[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000170852404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000170852404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC000170852404 none O=C(Nc1nnn[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 8, 8, 6, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 8, 10, 11, 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, 9, 9, 9, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 9, 5, 5, 5, 5] 10 rigid atoms, others: [1, 10, 11, 9] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 33) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(Nc1nnn[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000170852404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000170852404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC000170852404 none O=C(Nc1nnn[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 8, 8, 6, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 8, 10, 11, 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, 9, 9, 9, 9, 9, 1, 1, 1, 5, 5, 1, 1, 5, 5, 9, 5, 5, 5, 5] 10 rigid atoms, others: [1, 9, 10, 11] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000170852404 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000170852404 Building ZINC000175528157 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175528157 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/34 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nsc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC000175528157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175528157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000175528157 none CSc1nsc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 6, 28, 28, 28, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/35 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nsc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC000175528157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175528157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000175528157 none CSc1nsc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 6, 27, 27, 27, 4, 12, 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000175528157 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 Building ZINC000175528157 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175528157 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 34) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CSc1nsc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC000175528157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175528157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000175528157 none CSc1nsc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 6, 28, 28, 28, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 35) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CSc1nsc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC000175528157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175528157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000175528157 none CSc1nsc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 6, 27, 27, 27, 4, 12, 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000175528157 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000175528157 Building ZINC000658973344 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000658973344 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/36 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/36' -> `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)N1CC[C@@H](C)[C@@H](N)C1) `ZINC000658973344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000658973344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000658973344 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 17, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 47 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 70 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/37 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/37' -> `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)N1CC[C@@H](C)[C@@H](N)C1) `ZINC000658973344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000658973344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000658973344 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 16, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 44 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 60 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000658973344 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 Building ZINC000658973344 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000658973344 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 36) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H](N)C1) `ZINC000658973344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000658973344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000658973344 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 17, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 47 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 70 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 37) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H](N)C1) `ZINC000658973344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000658973344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000658973344 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 16, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 44 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 60 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000658973344 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000658973344 Building ZINC000162096526 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000162096526 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/38 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](N)CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000162096526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000162096526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000162096526 none CC(C)[C@H](N)CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 13, 27, 27, 11, 5, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 27, 27, 14, 14, 11, 11, 5, 5, 5, 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]) total number of confs: 155 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/39 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](N)CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000162096526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000162096526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000162096526 none CC(C)[C@H](N)CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 30, 12, 25, 25, 8, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 30, 31, 25, 25, 13, 13, 8, 8, 3, 3, 3, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000162096526 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 Building ZINC000162096526 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000162096526 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 38) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)[C@H](N)CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000162096526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000162096526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000162096526 none CC(C)[C@H](N)CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 13, 27, 27, 11, 5, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 27, 27, 14, 14, 11, 11, 5, 5, 5, 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]) total number of confs: 155 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 39) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)[C@H](N)CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000162096526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000162096526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000162096526 none CC(C)[C@H](N)CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 30, 12, 25, 25, 8, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 30, 31, 25, 25, 13, 13, 8, 8, 3, 3, 3, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000162096526 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162096526 Building ZINC000376492502 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000376492502 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/40 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000376492502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492502 none C[C@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 34, 34, 34, 34, 13, 13, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 13, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 13, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/41 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000376492502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492502 none C[C@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 29, 29, 29, 29, 13, 13, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 66 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000376492502 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 Building ZINC000376492502 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000376492502 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 40) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000376492502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492502 none C[C@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 34, 34, 34, 34, 13, 13, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 13, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 13, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 41) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000376492502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492502 none C[C@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 29, 29, 29, 29, 13, 13, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 66 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000376492502 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492502 Building ZINC000376492503 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000376492503 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/42 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000376492503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492503 none C[C@@H]1[C@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 30, 30, 30, 30, 13, 13, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/43 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000376492503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492503 none C[C@@H]1[C@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 34, 34, 34, 34, 13, 13, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 13, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 13, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000376492503 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 Building ZINC000376492503 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000376492503 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 42) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1[C@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000376492503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492503 none C[C@@H]1[C@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 30, 30, 30, 30, 13, 13, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 43) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1[C@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000376492503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492503 none C[C@@H]1[C@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 34, 34, 34, 34, 13, 13, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 13, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 13, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000376492503 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492503 Building ZINC000376492504 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000376492504 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/44 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000376492504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492504 none C[C@H]1[C@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 17, 31, 31, 31, 30, 14, 14, 8, 1, 8, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 14, 14, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/45 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000376492504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492504 none C[C@H]1[C@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 19, 31, 31, 31, 31, 17, 17, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 17, 17, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 64 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000376492504 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 Building ZINC000376492504 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000376492504 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 44) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1[C@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000376492504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492504 none C[C@H]1[C@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 17, 31, 31, 31, 30, 14, 14, 8, 1, 8, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 14, 14, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 45) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1[C@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000376492504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492504 none C[C@H]1[C@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 19, 31, 31, 31, 31, 17, 17, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 17, 17, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 64 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000376492504 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492504 Building ZINC000376492505 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000376492505 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/46 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000376492505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492505 none C[C@@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 18, 32, 32, 32, 31, 17, 17, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 17, 17, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/47 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000376492505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492505 none C[C@@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 18, 30, 30, 30, 29, 15, 15, 9, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000376492505 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 Building ZINC000376492505 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000376492505 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 46) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000376492505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492505 none C[C@@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 18, 32, 32, 32, 31, 17, 17, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 17, 17, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 47) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000376492505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000376492505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000376492505 none C[C@@H]1[C@@H](N2CCCC2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 18, 30, 30, 30, 29, 15, 15, 9, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000376492505 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000376492505 Building ZINC000647576958 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647576958 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/48 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1) `ZINC000647576958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647576958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000647576958 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 27, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 21, 21, 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/49 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1) `ZINC000647576958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647576958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000647576958 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 28, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 23, 23, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647576958 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 Building ZINC000647576958 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647576958 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 48) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1) `ZINC000647576958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647576958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000647576958 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 27, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 21, 21, 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 49) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1) `ZINC000647576958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647576958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000647576958 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 28, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 23, 23, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647576958 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576958 Building ZINC000647576959 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647576959 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/50 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1) `ZINC000647576959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647576959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000647576959 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/51 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1) `ZINC000647576959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647576959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000647576959 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 29, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 22, 22, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647576959 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 Building ZINC000647576959 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647576959 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 50) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1) `ZINC000647576959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647576959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000647576959 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 51) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1) `ZINC000647576959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647576959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000647576959 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 29, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 22, 22, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647576959 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647576959 Building ZINC000163668765 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000163668765 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/52 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000163668765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000163668765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000163668765 none CC(C)COC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 27, 30, 11, 10, 7, 10, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 27, 27, 7, 7, 7, 2, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/53 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000163668765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000163668765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000163668765 none CC(C)COC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 23, 34, 9, 9, 7, 9, 3, 7, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 23, 23, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000163668765 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 Building ZINC000163668765 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000163668765 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 52) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)COC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000163668765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000163668765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000163668765 none CC(C)COC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 27, 30, 11, 10, 7, 10, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 27, 27, 7, 7, 7, 2, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 53) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)COC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000163668765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000163668765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000163668765 none CC(C)COC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 23, 34, 9, 9, 7, 9, 3, 7, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 23, 23, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000163668765 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000163668765 Building ZINC000659211868 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000659211868 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/54 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/54' -> `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@](C)(CCF)C(=O)O) `ZINC000659211868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000659211868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000659211868 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@](C)(CCF)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 18, 18, 44, 45, 18, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 18, 18, 18, 44, 44, 45, 45, 90] 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]) total number of confs: 327 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/55 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/55' -> `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@](C)(CCF)C(=O)O) `ZINC000659211868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000659211868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000659211868 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@](C)(CCF)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 19, 19, 46, 47, 19, 33, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 19, 19, 19, 46, 46, 47, 47, 99] 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]) total number of confs: 348 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000659211868 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 Building ZINC000659211868 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000659211868 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 54) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@](C)(CCF)C(=O)O) `ZINC000659211868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000659211868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000659211868 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@](C)(CCF)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 18, 18, 44, 45, 18, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 18, 18, 18, 44, 44, 45, 45, 90] 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]) total number of confs: 327 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 55) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@](C)(CCF)C(=O)O) `ZINC000659211868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000659211868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000659211868 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@](C)(CCF)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 19, 19, 46, 47, 19, 33, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 19, 19, 19, 46, 46, 47, 47, 99] 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]) total number of confs: 348 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000659211868 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211868 Building ZINC000659211869 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000659211869 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/56 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/56' -> `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@@](C)(CCF)C(=O)O) `ZINC000659211869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000659211869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000659211869 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@](C)(CCF)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 18, 18, 46, 47, 18, 34, 34, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 18, 18, 18, 46, 46, 47, 47, 102] 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]) total number of confs: 365 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/57 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/57' -> `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@@](C)(CCF)C(=O)O) `ZINC000659211869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000659211869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000659211869 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@](C)(CCF)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 18, 18, 44, 45, 18, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 18, 18, 18, 44, 44, 45, 45, 90] 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]) total number of confs: 327 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000659211869 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 Building ZINC000659211869 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000659211869 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 56) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@](C)(CCF)C(=O)O) `ZINC000659211869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000659211869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000659211869 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@](C)(CCF)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 18, 18, 46, 47, 18, 34, 34, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 18, 18, 18, 46, 46, 47, 47, 102] 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]) total number of confs: 365 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 57) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@](C)(CCF)C(=O)O) `ZINC000659211869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000659211869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000659211869 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@](C)(CCF)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 18, 18, 44, 45, 18, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 18, 18, 18, 44, 44, 45, 45, 90] 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]) total number of confs: 327 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000659211869 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659211869 Building ZINC000782883533 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000782883533 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/58 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@@H]1C) `ZINC000782883533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000782883533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000782883533 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 2, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/59 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@@H]1C) `ZINC000782883533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000782883533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000782883533 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 1, 2, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000782883533 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 Building ZINC000782883533 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000782883533 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 58) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@@H]1C) `ZINC000782883533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000782883533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000782883533 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 2, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 59) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@@H]1C) `ZINC000782883533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000782883533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000782883533 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 1, 2, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000782883533 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883533 Building ZINC000782883537 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000782883537 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/60 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@H]1C) `ZINC000782883537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000782883537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000782883537 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 9, 9, 9, 1, 9, 9, 1, 1, 1, 2, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 48 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/61 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@H]1C) `ZINC000782883537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000782883537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000782883537 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000782883537 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 Building ZINC000782883537 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000782883537 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 60) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@H]1C) `ZINC000782883537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000782883537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000782883537 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 9, 9, 9, 1, 9, 9, 1, 1, 1, 2, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 48 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 61) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@H]1C) `ZINC000782883537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000782883537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000782883537 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000782883537 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000782883537 Building ZINC000178252243 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178252243 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/62 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CC(=O)O)cn1) `ZINC000178252243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178252243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178252243 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 1, 1, 1, 1, 4, 4, 4, 12, 12, 4, 12, 12, 12, 22, 31, 31, 10, 10, 10, 10, 10, 10, 4, 12, 12, 4, 12, 22, 22, 93, 10] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 224 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/63 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CC(=O)O)cn1) `ZINC000178252243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178252243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178252243 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 22, 29, 29, 10, 10, 10, 10, 10, 10, 4, 12, 12, 12, 12, 22, 22, 87, 10] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 198 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178252243 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 Building ZINC000178252243 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178252243 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 62) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CC(=O)O)cn1) `ZINC000178252243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178252243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178252243 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 1, 1, 1, 1, 4, 4, 4, 12, 12, 4, 12, 12, 12, 22, 31, 31, 10, 10, 10, 10, 10, 10, 4, 12, 12, 4, 12, 22, 22, 93, 10] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 224 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 63) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CC(=O)O)cn1) `ZINC000178252243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178252243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178252243 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 22, 29, 29, 10, 10, 10, 10, 10, 10, 4, 12, 12, 12, 12, 22, 22, 87, 10] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 198 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178252243 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178252243 Building ZINC000178256766 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178256766 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/64 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(C(=O)O)cc2)cn1) `ZINC000178256766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178256766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178256766 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(C(=O)O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 12, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 14, 25, 32, 32, 28, 28, 6, 6, 6, 6, 6, 6, 2, 14, 14, 28, 28, 96, 28, 28, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 261 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/65 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(C(=O)O)cc2)cn1) `ZINC000178256766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178256766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178256766 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(C(=O)O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 12, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 17, 26, 34, 34, 26, 26, 6, 6, 6, 6, 6, 6, 3, 15, 15, 26, 26, 102, 26, 26, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 256 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178256766 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 Building ZINC000178256766 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178256766 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 64) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(C(=O)O)cc2)cn1) `ZINC000178256766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178256766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178256766 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(C(=O)O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 12, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 14, 25, 32, 32, 28, 28, 6, 6, 6, 6, 6, 6, 2, 14, 14, 28, 28, 96, 28, 28, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 261 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 65) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(C(=O)O)cc2)cn1) `ZINC000178256766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178256766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178256766 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(C(=O)O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 12, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 17, 26, 34, 34, 26, 26, 6, 6, 6, 6, 6, 6, 3, 15, 15, 26, 26, 102, 26, 26, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 256 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178256766 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178256766 Building ZINC000659376428 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000659376428 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/66 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CCCN) `ZINC000659376428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000659376428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000659376428 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CCCN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 19, 22, 31, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 19, 19, 22, 22, 31, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/67 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CCCN) `ZINC000659376428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000659376428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000659376428 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CCCN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 18, 21, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 18, 18, 21, 21, 28, 28, 28, 28] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 126 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000659376428 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 Building ZINC000659376428 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000659376428 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 66) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CCCN) `ZINC000659376428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000659376428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000659376428 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CCCN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 19, 22, 31, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 19, 19, 22, 22, 31, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 67) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CCCN) `ZINC000659376428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000659376428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000659376428 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CCCN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 18, 21, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 18, 18, 21, 21, 28, 28, 28, 28] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 126 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000659376428 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659376428 Building ZINC000407974531 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000407974531 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/68 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC2)cn1) `ZINC000407974531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000407974531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000407974531 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 18, 18, 8, 8, 1, 1, 1, 1, 7, 8, 15, 15, 15, 15, 15, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 15, 15, 15, 15, 15, 15, 15, 15, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/69 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOCC2)cn1) `ZINC000407974531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000407974531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000407974531 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 10, 23, 23, 10, 10, 1, 1, 1, 1, 7, 9, 18, 18, 18, 18, 18, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10] 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]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000407974531 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 Building ZINC000407974531 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000407974531 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 68) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC2)cn1) `ZINC000407974531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000407974531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000407974531 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 18, 18, 8, 8, 1, 1, 1, 1, 7, 8, 15, 15, 15, 15, 15, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 15, 15, 15, 15, 15, 15, 15, 15, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 69) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOCC2)cn1) `ZINC000407974531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000407974531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000407974531 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 10, 23, 23, 10, 10, 1, 1, 1, 1, 7, 9, 18, 18, 18, 18, 18, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10] 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]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000407974531 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407974531 Building ZINC000407978766 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000407978766 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/70 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/70' -> `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(O)CC2)cn1) `ZINC000407978766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000407978766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000407978766 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 12, 12, 12, 12, 12, 36, 12, 12, 12, 12, 9] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/71 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/71' -> `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(O)CC2)cn1) `ZINC000407978766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000407978766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000407978766 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 18, 18, 10, 10, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 12, 12, 12, 12, 12, 36, 12, 12, 12, 12, 10] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000407978766 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 Building ZINC000407978766 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000407978766 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 70) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(O)CC2)cn1) `ZINC000407978766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000407978766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000407978766 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 12, 12, 12, 12, 12, 36, 12, 12, 12, 12, 9] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 71) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(O)CC2)cn1) `ZINC000407978766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000407978766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000407978766 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 18, 18, 10, 10, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 12, 12, 12, 12, 12, 36, 12, 12, 12, 12, 10] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000407978766 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000407978766 Building ZINC001075520495 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001075520495 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/72 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@@H]1CCCO1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001075520495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001075520495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001075520495 none C[C@@H](CCNC(=O)[C@@H]1CCCO1)NC(=O)[C@@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 21, 36, 36, 37, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 21, 21, 36, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/73 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@@H]1CCCO1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001075520495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001075520495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001075520495 none C[C@@H](CCNC(=O)[C@@H]1CCCO1)NC(=O)[C@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 14, 24, 33, 33, 37, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 24, 23, 33, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001075520495 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 Building ZINC001075520495 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001075520495 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 72) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](CCNC(=O)[C@@H]1CCCO1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001075520495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001075520495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001075520495 none C[C@@H](CCNC(=O)[C@@H]1CCCO1)NC(=O)[C@@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 21, 36, 36, 37, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 21, 21, 36, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 73) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](CCNC(=O)[C@@H]1CCCO1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001075520495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001075520495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001075520495 none C[C@@H](CCNC(=O)[C@@H]1CCCO1)NC(=O)[C@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 14, 24, 33, 33, 37, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 24, 23, 33, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001075520495 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520495 Building ZINC001075520496 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001075520496 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/74 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@H]1CCCO1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001075520496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001075520496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001075520496 none C[C@@H](CCNC(=O)[C@H]1CCCO1)NC(=O)[C@@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 11, 18, 38, 38, 43, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 18, 18, 38, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/75 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@H]1CCCO1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001075520496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001075520496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001075520496 none C[C@@H](CCNC(=O)[C@H]1CCCO1)NC(=O)[C@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 20, 31, 31, 41, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 20, 20, 31, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001075520496 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 Building ZINC001075520496 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001075520496 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 74) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](CCNC(=O)[C@H]1CCCO1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001075520496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001075520496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001075520496 none C[C@@H](CCNC(=O)[C@H]1CCCO1)NC(=O)[C@@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 11, 18, 38, 38, 43, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 18, 18, 38, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 75) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](CCNC(=O)[C@H]1CCCO1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001075520496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001075520496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001075520496 none C[C@@H](CCNC(=O)[C@H]1CCCO1)NC(=O)[C@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 20, 31, 31, 41, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 20, 20, 31, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001075520496 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001075520496 Building ZINC000178522437 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178522437 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/76 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000178522437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178522437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178522437 none NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 15, 15, 15, 15, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 15, 27, 27, 27, 27, 15, 15, 15, 15, 6, 10, 10, 6, 10, 10, 6, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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/170854/xdl-8058088.90/working/building/ZINC000178522437 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/77 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000178522437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178522437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178522437 none NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 17, 17, 17, 17, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 17, 30, 30, 30, 30, 17, 17, 17, 17, 6, 10, 10, 6, 10, 10, 6, 17, 17] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178522437 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437 Building ZINC000178522437 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178522437 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 76) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000178522437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178522437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178522437 none NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 15, 15, 15, 15, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 15, 27, 27, 27, 27, 15, 15, 15, 15, 6, 10, 10, 6, 10, 10, 6, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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/170854/xdl-8058088.90/working/building/ZINC000178522437 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 77) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000178522437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178522437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178522437 none NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 17, 17, 17, 17, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 17, 30, 30, 30, 30, 17, 17, 17, 17, 6, 10, 10, 6, 10, 10, 6, 17, 17] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178522437 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522437 Building ZINC000178522449 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178522449 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/78 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000178522449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178522449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178522449 none NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 14, 14, 14, 14, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 14, 27, 27, 27, 27, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 6, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/79 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000178522449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178522449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178522449 none NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 15, 15, 15, 15, 4, 1, 7, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 15, 29, 29, 29, 29, 15, 15, 15, 15, 6, 12, 12, 6, 12, 12, 6, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178522449 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 Building ZINC000178522449 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178522449 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 78) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000178522449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178522449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178522449 none NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 14, 14, 14, 14, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 14, 27, 27, 27, 27, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 6, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 79) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000178522449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178522449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178522449 none NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 15, 15, 15, 15, 4, 1, 7, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 15, 29, 29, 29, 29, 15, 15, 15, 15, 6, 12, 12, 6, 12, 12, 6, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178522449 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178522449 Building ZINC000647651907 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647651907 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/80 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000647651907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647651907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000647651907 none Cc1nccn1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 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, 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] 0 hydrogens 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, 21, 16, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 39, 39, 39, 39, 39, 21, 21, 21, 21, 13, 13, 2, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/81 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CCCNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000647651907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647651907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000647651907 none Cc1nccn1CCCNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 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, 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] 0 hydrogens 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, 21, 16, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 39, 39, 39, 39, 39, 21, 21, 21, 21, 13, 13, 2, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647651907 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 Building ZINC000647651907 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647651907 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 80) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nccn1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000647651907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647651907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000647651907 none Cc1nccn1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 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, 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] 0 hydrogens 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, 21, 16, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 39, 39, 39, 39, 39, 21, 21, 21, 21, 13, 13, 2, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 81) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nccn1CCCNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000647651907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647651907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000647651907 none Cc1nccn1CCCNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 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, 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] 0 hydrogens 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, 21, 16, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 39, 39, 39, 39, 39, 21, 21, 21, 21, 13, 13, 2, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647651907 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647651907 Building ZINC000178621858 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178621858 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/82 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178621858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178621858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000178621858 none C[C@H](N)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 7] 0 hydrogens 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, 27, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 20, 20, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/83 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178621858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178621858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000178621858 none C[C@H](N)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 7] 0 hydrogens 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, 32, 32, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 23, 23, 14, 14, 2, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178621858 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 Building ZINC000178621858 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178621858 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 82) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H](N)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178621858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178621858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000178621858 none C[C@H](N)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 7] 0 hydrogens 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, 27, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 20, 20, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 83) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H](N)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178621858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178621858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000178621858 none C[C@H](N)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 7] 0 hydrogens 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, 32, 32, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 23, 23, 14, 14, 2, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178621858 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621858 Building ZINC000178621870 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178621870 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/84 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178621870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178621870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000178621870 none C[C@@H](N)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 34, 34, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 34, 34, 34, 34, 34, 19, 19, 13, 13, 2, 6, 7, 7, 6, 7, 7, 6] 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/85 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178621870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178621870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000178621870 none C[C@@H](N)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 32, 32, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 32, 32, 32, 32, 32, 18, 18, 11, 11, 2, 6, 8, 8, 6, 8, 8, 6] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178621870 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 Building ZINC000178621870 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178621870 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 84) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](N)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178621870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178621870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000178621870 none C[C@@H](N)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 34, 34, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 34, 34, 34, 34, 34, 19, 19, 13, 13, 2, 6, 7, 7, 6, 7, 7, 6] 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 85) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](N)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178621870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178621870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000178621870 none C[C@@H](N)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 32, 32, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 32, 32, 32, 32, 32, 18, 18, 11, 11, 2, 6, 8, 8, 6, 8, 8, 6] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178621870 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178621870 Building ZINC000178724408 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178724408 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/86 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178724408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178724408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178724408 none O=C(NC[C@@H]1CCCN1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 32, 32, 32, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/87 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178724408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178724408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178724408 none O=C(NC[C@@H]1CCCN1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178724408 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 Building ZINC000178724408 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178724408 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 86) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(NC[C@@H]1CCCN1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178724408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178724408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178724408 none O=C(NC[C@@H]1CCCN1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 32, 32, 32, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 87) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(NC[C@@H]1CCCN1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178724408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178724408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178724408 none O=C(NC[C@@H]1CCCN1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178724408 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724408 Building ZINC000178724418 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178724418 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/88 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178724418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178724418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178724418 none O=C(NC[C@H]1CCCN1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/89 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178724418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178724418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178724418 none O=C(NC[C@H]1CCCN1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178724418 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 Building ZINC000178724418 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178724418 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 88) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(NC[C@H]1CCCN1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178724418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178724418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178724418 none O=C(NC[C@H]1CCCN1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 89) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(NC[C@H]1CCCN1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000178724418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178724418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000178724418 none O=C(NC[C@H]1CCCN1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000178724418 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000178724418 Building ZINC000652005467 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000652005467 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/90 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 17, 18, 18, 18, 18, 31, 46, 46, 18, 1, 1, 1, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 31, 31, 46, 46, 46, 46, 46, 18, 18, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/91 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 7, 19, 19, 19, 19, 19, 31, 43, 43, 19, 1, 1, 1, 3, 3, 3, 3, 3, 2, 19, 19, 19, 19, 31, 31, 43, 43, 43, 43, 43, 19, 19, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/92 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/92' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 17, 18, 18, 18, 18, 31, 46, 46, 18, 1, 1, 1, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 31, 31, 46, 46, 46, 46, 46, 18, 18, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/93 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/93' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 7, 19, 19, 19, 19, 19, 31, 43, 43, 19, 1, 1, 1, 3, 3, 3, 3, 3, 2, 19, 19, 19, 19, 31, 31, 43, 43, 43, 43, 43, 19, 19, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652005467 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 Building ZINC000652005467 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000652005467 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 90) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 17, 18, 18, 18, 18, 31, 46, 46, 18, 1, 1, 1, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 31, 31, 46, 46, 46, 46, 46, 18, 18, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 91) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 7, 19, 19, 19, 19, 19, 31, 43, 43, 19, 1, 1, 1, 3, 3, 3, 3, 3, 2, 19, 19, 19, 19, 31, 31, 43, 43, 43, 43, 43, 19, 19, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 92) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 17, 18, 18, 18, 18, 31, 46, 46, 18, 1, 1, 1, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 31, 31, 46, 46, 46, 46, 46, 18, 18, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 93) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 7, 19, 19, 19, 19, 19, 31, 43, 43, 19, 1, 1, 1, 3, 3, 3, 3, 3, 2, 19, 19, 19, 19, 31, 31, 43, 43, 43, 43, 43, 19, 19, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652005467 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 Building ZINC000652005467 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000652005467 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 90) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 17, 18, 18, 18, 18, 31, 46, 46, 18, 1, 1, 1, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 31, 31, 46, 46, 46, 46, 46, 18, 18, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 91) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 7, 19, 19, 19, 19, 19, 31, 43, 43, 19, 1, 1, 1, 3, 3, 3, 3, 3, 2, 19, 19, 19, 19, 31, 31, 43, 43, 43, 43, 43, 19, 19, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 92) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 17, 18, 18, 18, 18, 31, 46, 46, 18, 1, 1, 1, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 31, 31, 46, 46, 46, 46, 46, 18, 18, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 93) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 7, 19, 19, 19, 19, 19, 31, 43, 43, 19, 1, 1, 1, 3, 3, 3, 3, 3, 2, 19, 19, 19, 19, 31, 31, 43, 43, 43, 43, 43, 19, 19, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652005467 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 Building ZINC000652005467 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000652005467 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 90) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 17, 18, 18, 18, 18, 31, 46, 46, 18, 1, 1, 1, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 31, 31, 46, 46, 46, 46, 46, 18, 18, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 91) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 7, 19, 19, 19, 19, 19, 31, 43, 43, 19, 1, 1, 1, 3, 3, 3, 3, 3, 2, 19, 19, 19, 19, 31, 31, 43, 43, 43, 43, 43, 19, 19, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 92) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 17, 18, 18, 18, 18, 31, 46, 46, 18, 1, 1, 1, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 31, 31, 46, 46, 46, 46, 46, 18, 18, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 93) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652005467.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000652005467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000652005467 none O=C(N[C@@H]1CCN(CC2CC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 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] 0 hydrogens need rotated 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, 7, 19, 19, 19, 19, 19, 31, 43, 43, 19, 1, 1, 1, 3, 3, 3, 3, 3, 2, 19, 19, 19, 19, 31, 31, 43, 43, 43, 43, 43, 19, 19, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652005467 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652005467 Building ZINC000647655151 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647655151 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/94 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(C)(C)C)C2=O)cn1) `ZINC000647655151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647655151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000647655151 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(C)(C)C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 7, 17, 17, 17, 17, 17, 29, 29, 29, 17, 17, 10, 10, 10, 10, 10, 10, 4, 17, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/95 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(C)(C)C)C2=O)cn1) `ZINC000647655151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647655151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000647655151 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(C)(C)C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 28, 28, 28, 17, 17, 9, 9, 9, 9, 9, 9, 5, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647655151 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 Building ZINC000647655151 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647655151 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 94) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(C)(C)C)C2=O)cn1) `ZINC000647655151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647655151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000647655151 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(C)(C)C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 7, 17, 17, 17, 17, 17, 29, 29, 29, 17, 17, 10, 10, 10, 10, 10, 10, 4, 17, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 95) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(C)(C)C)C2=O)cn1) `ZINC000647655151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647655151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000647655151 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(C)(C)C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 28, 28, 28, 17, 17, 9, 9, 9, 9, 9, 9, 5, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647655151 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647655151 Building ZINC000353632598 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353632598 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/96 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c2n[nH]c(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)c12) `ZINC000353632598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353632598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000353632598 none Cc1nn(C)c2n[nH]c(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)c12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 37, 37, 22, 11, 1, 11, 1, 1, 1, 8, 8, 8, 8, 8, 37, 37, 37, 37, 37, 37, 37, 22, 8, 8, 8, 8, 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]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/97 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c2n[nH]c(NC(=O)[C@]([O-])([SiH3])c3cccn3C)c12) `ZINC000353632598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353632598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000353632598 none Cc1nn(C)c2n[nH]c(NC(=O)[C@]([O-])([SiH3])c3cccn3C)c12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 23, 11, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 23, 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]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000353632598 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 Building ZINC000353632598 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353632598 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 96) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(C)c2n[nH]c(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)c12) `ZINC000353632598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353632598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000353632598 none Cc1nn(C)c2n[nH]c(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)c12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 37, 37, 22, 11, 1, 11, 1, 1, 1, 8, 8, 8, 8, 8, 37, 37, 37, 37, 37, 37, 37, 22, 8, 8, 8, 8, 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]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 97) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(C)c2n[nH]c(NC(=O)[C@]([O-])([SiH3])c3cccn3C)c12) `ZINC000353632598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353632598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000353632598 none Cc1nn(C)c2n[nH]c(NC(=O)[C@]([O-])([SiH3])c3cccn3C)c12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 23, 11, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 23, 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]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000353632598 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353632598 Building ZINC000179186341 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179186341 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/98 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000179186341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179186341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179186341 none C[C@@H](CN)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 7, 21, 21, 29, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 21, 21, 21, 29, 29, 29, 29, 7, 7, 7, 6, 14, 14, 6, 14, 14, 6] 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]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/99 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000179186341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179186341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179186341 none C[C@@H](CN)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 22, 4, 6, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 13, 13, 13, 22, 22, 22, 22, 6, 6, 6, 6, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000179186341 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 Building ZINC000179186341 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179186341 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 98) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](CN)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000179186341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179186341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179186341 none C[C@@H](CN)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 7, 21, 21, 29, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 21, 21, 21, 29, 29, 29, 29, 7, 7, 7, 6, 14, 14, 6, 14, 14, 6] 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]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 99) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](CN)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000179186341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179186341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179186341 none C[C@@H](CN)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 22, 4, 6, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 13, 13, 13, 22, 22, 22, 22, 6, 6, 6, 6, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000179186341 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186341 Building ZINC000179186350 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179186350 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/100 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000179186350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179186350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179186350 none C[C@H](CN)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 29, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 16, 16, 16, 29, 29, 29, 29, 7, 7, 7, 6, 14, 14, 6, 14, 14, 6] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/101 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000179186350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179186350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179186350 none C[C@H](CN)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 23, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 16, 16, 16, 23, 23, 23, 23, 7, 7, 7, 6, 14, 14, 6, 14, 14, 6] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000179186350 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 Building ZINC000179186350 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179186350 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 100) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000179186350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179186350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179186350 none C[C@H](CN)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 29, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 16, 16, 16, 29, 29, 29, 29, 7, 7, 7, 6, 14, 14, 6, 14, 14, 6] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 101) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000179186350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179186350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179186350 none C[C@H](CN)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 23, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 16, 16, 16, 23, 23, 23, 23, 7, 7, 7, 6, 14, 14, 6, 14, 14, 6] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000179186350 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179186350 Building ZINC000408006882 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408006882 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/102 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCCO1) `ZINC000408006882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408006882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000408006882 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 12, 7, 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, 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] 0 hydrogens 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, 2, 19, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/103 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCCO1) `ZINC000408006882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408006882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000408006882 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 12, 7, 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, 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] 0 hydrogens 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, 23, 2, 24, 1, 1, 1, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408006882 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 Building ZINC000408006882 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408006882 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 102) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCCO1) `ZINC000408006882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408006882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000408006882 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 12, 7, 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, 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] 0 hydrogens 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, 2, 19, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 103) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCCO1) `ZINC000408006882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408006882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000408006882 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 12, 7, 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, 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] 0 hydrogens 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, 23, 2, 24, 1, 1, 1, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408006882 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006882 Building ZINC000408006884 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408006884 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/104 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCCO1) `ZINC000408006884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408006884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000408006884 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 12, 7, 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, 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] 0 hydrogens 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, 26, 1, 26, 1, 1, 1, 10, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/105 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCCO1) `ZINC000408006884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408006884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000408006884 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 12, 7, 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, 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] 0 hydrogens 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, 19, 1, 19, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408006884 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 Building ZINC000408006884 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408006884 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 104) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCCO1) `ZINC000408006884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408006884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000408006884 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 12, 7, 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, 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] 0 hydrogens 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, 26, 1, 26, 1, 1, 1, 10, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 105) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCCO1) `ZINC000408006884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408006884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000408006884 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 12, 7, 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, 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] 0 hydrogens 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, 19, 1, 19, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408006884 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408006884 Building ZINC000353633722 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353633722 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/106 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)C1=O) `ZINC000353633722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353633722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000353633722 none CC(C)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'N.pl3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 45, 24, 24, 24, 9, 24, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 45, 45, 45, 45, 45, 45, 45, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/107 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)C1=O) `ZINC000353633722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353633722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000353633722 none CC(C)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'N.pl3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 42, 24, 24, 24, 9, 24, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 24, 24, 42, 42, 42, 42, 42, 42, 42, 24, 24, 24, 24, 5, 6, 6, 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000353633722 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 Building ZINC000353633722 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353633722 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 106) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)C1=O) `ZINC000353633722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353633722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000353633722 none CC(C)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'N.pl3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 45, 24, 24, 24, 9, 24, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 45, 45, 45, 45, 45, 45, 45, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 107) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)C1=O) `ZINC000353633722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353633722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000353633722 none CC(C)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'N.pl3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 42, 24, 24, 24, 9, 24, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 24, 24, 42, 42, 42, 42, 42, 42, 42, 24, 24, 24, 24, 5, 6, 6, 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000353633722 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353633722 Building ZINC000408014839 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408014839 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/108 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/108' -> `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](O)C2)cn1) `ZINC000408014839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408014839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408014839 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 2, 8, 9, 14, 14, 14, 14, 14, 14, 14, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 14, 14, 14, 14, 14, 14, 42, 14, 14, 6] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/109 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/109' -> `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](O)C2)cn1) `ZINC000408014839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408014839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408014839 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 12, 12, 5, 5, 1, 1, 1, 2, 6, 8, 13, 13, 13, 13, 13, 13, 13, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 13, 13, 13, 13, 13, 13, 39, 13, 13, 5] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408014839 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 Building ZINC000408014839 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408014839 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 108) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)C2)cn1) `ZINC000408014839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408014839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408014839 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 2, 8, 9, 14, 14, 14, 14, 14, 14, 14, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 14, 14, 14, 14, 14, 14, 42, 14, 14, 6] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 109) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)C2)cn1) `ZINC000408014839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408014839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408014839 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 12, 12, 5, 5, 1, 1, 1, 2, 6, 8, 13, 13, 13, 13, 13, 13, 13, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 13, 13, 13, 13, 13, 13, 39, 13, 13, 5] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408014839 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014839 Building ZINC000408014840 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408014840 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/110 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/110' -> `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](O)C2)cn1) `ZINC000408014840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408014840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408014840 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 2, 8, 9, 14, 14, 14, 14, 14, 14, 14, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 14, 14, 14, 14, 14, 14, 42, 14, 14, 6] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/111 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/111' -> `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](O)C2)cn1) `ZINC000408014840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408014840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408014840 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 11, 11, 6, 6, 1, 1, 1, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 13, 13, 13, 13, 13, 13, 39, 13, 13, 6] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408014840 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 Building ZINC000408014840 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408014840 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 110) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](O)C2)cn1) `ZINC000408014840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408014840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408014840 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 2, 8, 9, 14, 14, 14, 14, 14, 14, 14, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 14, 14, 14, 14, 14, 14, 42, 14, 14, 6] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 111) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](O)C2)cn1) `ZINC000408014840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408014840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408014840 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 11, 11, 6, 6, 1, 1, 1, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 13, 13, 13, 13, 13, 13, 39, 13, 13, 6] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408014840 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408014840 Building ZINC000659775554 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000659775554 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/112 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CCC(=O)O)CC2)cn1) `ZINC000659775554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000659775554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000659775554 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CCC(=O)O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 19, 26, 33, 33, 5, 5, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 19, 19, 26, 26, 99, 5, 5, 5, 5, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/113 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CCC(=O)O)CC2)cn1) `ZINC000659775554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000659775554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000659775554 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CCC(=O)O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 18, 25, 40, 40, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 25, 25, 120, 6, 6, 6, 6, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 280 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000659775554 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 Building ZINC000659775554 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000659775554 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 112) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CCC(=O)O)CC2)cn1) `ZINC000659775554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000659775554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000659775554 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CCC(=O)O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 19, 26, 33, 33, 5, 5, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 19, 19, 26, 26, 99, 5, 5, 5, 5, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 113) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CCC(=O)O)CC2)cn1) `ZINC000659775554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000659775554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000659775554 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CCC(=O)O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 18, 25, 40, 40, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 25, 25, 120, 6, 6, 6, 6, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 280 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000659775554 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659775554 Building ZINC000659781951 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000659781951 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/114 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N(CC(=O)O)CC(C)(C)C)cn1) `ZINC000659781951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000659781951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000659781951 none Cn1cc([C@]([O-])([SiH3])C(=O)N(CC(=O)O)CC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 14, 23, 23, 7, 12, 16, 16, 16, 6, 6, 6, 6, 6, 6, 14, 14, 69, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 129 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/115 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N(CC(=O)O)CC(C)(C)C)cn1) `ZINC000659781951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000659781951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000659781951 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(CC(=O)O)CC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 6, 12, 19, 19, 6, 12, 18, 18, 18, 6, 6, 6, 6, 6, 6, 12, 12, 57, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 123 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 195 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000659781951 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 Building ZINC000659781951 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000659781951 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 114) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N(CC(=O)O)CC(C)(C)C)cn1) `ZINC000659781951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000659781951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000659781951 none Cn1cc([C@]([O-])([SiH3])C(=O)N(CC(=O)O)CC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 14, 23, 23, 7, 12, 16, 16, 16, 6, 6, 6, 6, 6, 6, 14, 14, 69, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 129 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 115) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N(CC(=O)O)CC(C)(C)C)cn1) `ZINC000659781951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000659781951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000659781951 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(CC(=O)O)CC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 6, 12, 19, 19, 6, 12, 18, 18, 18, 6, 6, 6, 6, 6, 6, 12, 12, 57, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 123 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 195 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000659781951 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000659781951 Building ZINC000408023289 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408023289 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/116 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/116' -> `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)N1CCc2n[nH]cc2C1) `ZINC000408023289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408023289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408023289 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21] 30 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 38 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/117 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/117' -> `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)N1CCc2n[nH]cc2C1) `ZINC000408023289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408023289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408023289 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22] 31 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 39 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408023289 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 Building ZINC000408023289 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408023289 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 116) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2n[nH]cc2C1) `ZINC000408023289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408023289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408023289 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21] 30 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 38 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 117) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2n[nH]cc2C1) `ZINC000408023289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408023289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408023289 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22] 31 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 39 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408023289 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408023289 Building ZINC000580260633 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000580260633 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/118 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000580260633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000580260633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000580260633 none O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [14, 2, 17, 29, 29, 29, 29, 29, 47, 29, 29, 29, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 47, 47, 141, 87, 29, 29, 3, 3, 3, 3] 450 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]) total number of confs: 395 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/119 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000580260633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000580260633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000580260633 none O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 16, 29, 29, 29, 29, 29, 46, 29, 29, 29, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 46, 46, 138, 87, 29, 29, 3, 3, 3, 3] 450 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]) total number of confs: 382 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000580260633 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 Building ZINC000580260633 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000580260633 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 118) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000580260633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000580260633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000580260633 none O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [14, 2, 17, 29, 29, 29, 29, 29, 47, 29, 29, 29, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 47, 47, 141, 87, 29, 29, 3, 3, 3, 3] 450 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]) total number of confs: 395 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 119) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000580260633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000580260633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000580260633 none O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 16, 29, 29, 29, 29, 29, 46, 29, 29, 29, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 46, 46, 138, 87, 29, 29, 3, 3, 3, 3] 450 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]) total number of confs: 382 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000580260633 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000580260633 Building ZINC000135427685 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000135427685 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/120 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c(O)c1) `ZINC000135427685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000135427685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000135427685 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c(O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 19, 28, 28, 28, 19, 19, 5, 12, 12, 12, 12, 12, 38, 19] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/121 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c(O)c1) `ZINC000135427685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000135427685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000135427685 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c(O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 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] 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, 20, 13, 20, 20, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 29, 29, 29, 20, 20, 5, 11, 11, 11, 11, 11, 40, 20] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000135427685 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 Building ZINC000135427685 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000135427685 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 120) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c(O)c1) `ZINC000135427685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000135427685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000135427685 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c(O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 19, 28, 28, 28, 19, 19, 5, 12, 12, 12, 12, 12, 38, 19] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 121) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c(O)c1) `ZINC000135427685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000135427685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000135427685 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c(O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 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] 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, 20, 13, 20, 20, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 29, 29, 29, 20, 20, 5, 11, 11, 11, 11, 11, 40, 20] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000135427685 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000135427685 Building ZINC000408033896 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408033896 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/122 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1C(C)(C)O) `ZINC000408033896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408033896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000408033896 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 36, 36, 36, 36, 36, 36, 108] 123 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 240 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/123 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1C(C)(C)O) `ZINC000408033896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408033896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000408033896 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 13, 38, 38, 38, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 38, 38, 38, 38, 38, 38, 114] 135 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 245 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408033896 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 Building ZINC000408033896 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408033896 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 122) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1C(C)(C)O) `ZINC000408033896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408033896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000408033896 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 36, 36, 36, 36, 36, 36, 108] 123 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 240 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 123) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1C(C)(C)O) `ZINC000408033896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408033896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000408033896 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 13, 38, 38, 38, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 38, 38, 38, 38, 38, 38, 114] 135 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 245 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408033896 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033896 Building ZINC000408033897 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408033897 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/124 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1C(C)(C)O) `ZINC000408033897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408033897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000408033897 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 42, 42, 42, 42, 42, 42, 126] 147 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 270 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/125 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1C(C)(C)O) `ZINC000408033897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408033897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000408033897 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 37, 37, 37, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 37, 37, 37, 37, 37, 37, 111] 126 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 245 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408033897 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 Building ZINC000408033897 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408033897 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 124) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1C(C)(C)O) `ZINC000408033897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408033897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000408033897 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 42, 42, 42, 42, 42, 42, 126] 147 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 270 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 125) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1C(C)(C)O) `ZINC000408033897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408033897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000408033897 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 37, 37, 37, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 37, 37, 37, 37, 37, 37, 111] 126 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 245 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408033897 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408033897 Building ZINC000377123512 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377123512 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/126 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(O)(c3ccccc3)C2)cn1) `ZINC000377123512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377123512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000377123512 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(O)(c3ccccc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 6, 16, 16, 16, 16, 30, 30, 16, 30, 30, 16, 5, 5, 5, 5, 5, 5, 16, 16, 48, 30, 30, 16, 30, 30, 16, 16, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/127 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(O)(c3ccccc3)C2)cn1) `ZINC000377123512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377123512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000377123512 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(O)(c3ccccc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 3, 5, 18, 18, 18, 18, 31, 31, 18, 31, 31, 18, 4, 4, 4, 4, 4, 4, 18, 18, 54, 31, 31, 18, 31, 31, 18, 18, 4] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000377123512 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 Building ZINC000377123512 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377123512 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 126) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(O)(c3ccccc3)C2)cn1) `ZINC000377123512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377123512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000377123512 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(O)(c3ccccc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 6, 16, 16, 16, 16, 30, 30, 16, 30, 30, 16, 5, 5, 5, 5, 5, 5, 16, 16, 48, 30, 30, 16, 30, 30, 16, 16, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 127) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(O)(c3ccccc3)C2)cn1) `ZINC000377123512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377123512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000377123512 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(O)(c3ccccc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 3, 5, 18, 18, 18, 18, 31, 31, 18, 31, 31, 18, 4, 4, 4, 4, 4, 4, 18, 18, 54, 31, 31, 18, 31, 31, 18, 18, 4] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000377123512 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377123512 Building ZINC000892775886 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000892775886 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/128 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1) `ZINC000892775886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000892775886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000892775886 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 30, 30, 30, 30, 30, 12, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/129 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1) `ZINC000892775886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000892775886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000892775886 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 29, 29, 29, 29, 29, 12, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000892775886 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 Building ZINC000892775886 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000892775886 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 128) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1) `ZINC000892775886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000892775886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000892775886 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 30, 30, 30, 30, 30, 12, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 129) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1) `ZINC000892775886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000892775886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000892775886 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 29, 29, 29, 29, 29, 12, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000892775886 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775886 Building ZINC000892775889 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000892775889 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/130 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1) `ZINC000892775889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000892775889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000892775889 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 29, 29, 29, 29, 29, 12, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/131 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1) `ZINC000892775889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000892775889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000892775889 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 30, 30, 30, 30, 30, 12, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000892775889 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 Building ZINC000892775889 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000892775889 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 130) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1) `ZINC000892775889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000892775889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000892775889 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 29, 29, 29, 29, 29, 12, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 131) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1) `ZINC000892775889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000892775889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000892775889 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 30, 30, 30, 30, 30, 12, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000892775889 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892775889 Building ZINC000377198913 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377198913 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/132 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(N)=O)C1) `ZINC000377198913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377198913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000377198913 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 33, 48, 48, 10, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 33, 33, 48, 48, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/133 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(N)=O)C1) `ZINC000377198913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377198913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000377198913 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 3, 11, 11, 11, 11, 11, 31, 47, 47, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 31, 31, 47, 47, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000377198913 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 Building ZINC000377198913 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377198913 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 132) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(N)=O)C1) `ZINC000377198913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377198913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000377198913 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 33, 48, 48, 10, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 33, 33, 48, 48, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 133) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(N)=O)C1) `ZINC000377198913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377198913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000377198913 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 3, 11, 11, 11, 11, 11, 31, 47, 47, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 31, 31, 47, 47, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000377198913 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198913 Building ZINC000377198914 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377198914 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/134 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CC(N)=O)C1) `ZINC000377198914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377198914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000377198914 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 3, 11, 11, 11, 11, 11, 31, 47, 47, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 31, 31, 47, 47, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/135 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CC(N)=O)C1) `ZINC000377198914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377198914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000377198914 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 33, 48, 48, 10, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 33, 33, 48, 48, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000377198914 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 Building ZINC000377198914 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377198914 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 134) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CC(N)=O)C1) `ZINC000377198914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377198914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000377198914 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 3, 11, 11, 11, 11, 11, 31, 47, 47, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 31, 31, 47, 47, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 135) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CC(N)=O)C1) `ZINC000377198914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377198914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000377198914 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 33, 48, 48, 10, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 33, 33, 48, 48, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000377198914 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377198914 Building ZINC000892786907 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000892786907 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/136 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1) `ZINC000892786907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000892786907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000892786907 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/137 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1) `ZINC000892786907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000892786907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000892786907 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000892786907 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 Building ZINC000892786907 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000892786907 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 136) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1) `ZINC000892786907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000892786907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000892786907 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 137) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1) `ZINC000892786907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000892786907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000892786907 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000892786907 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786907 Building ZINC000892786908 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000892786908 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/138 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1) `ZINC000892786908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000892786908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000892786908 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/139 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1) `ZINC000892786908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000892786908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000892786908 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000892786908 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 Building ZINC000892786908 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000892786908 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 138) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1) `ZINC000892786908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000892786908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000892786908 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 139) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1) `ZINC000892786908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000892786908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000892786908 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(C)CN3CCC2CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000892786908 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000892786908 Building ZINC000601222032 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000601222032 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/140 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000601222032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000601222032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000601222032 none COC(=O)[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7] 0 hydrogens 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, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 12, 32, 32, 32, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/141 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000601222032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000601222032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000601222032 none COC(=O)[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 14, 34, 14, 14, 14, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 14, 14, 34, 34, 34, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000601222032 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 Building ZINC000601222032 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000601222032 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 140) grep: /scratch/xiaobo/170854/xdl-8058088.90/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@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000601222032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000601222032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000601222032 none COC(=O)[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7] 0 hydrogens 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, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 12, 32, 32, 32, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 141) grep: /scratch/xiaobo/170854/xdl-8058088.90/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@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000601222032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000601222032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000601222032 none COC(=O)[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 14, 34, 14, 14, 14, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 14, 14, 34, 34, 34, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000601222032 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000601222032 Building ZINC000151975008 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000151975008 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/142 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)C1) `ZINC000151975008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000151975008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000151975008 none CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 29, 41, 29, 29, 29, 11, 29, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 41, 41, 41, 29, 29, 29, 29, 6, 5, 5, 5, 5, 5, 5, 5, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/143 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)C1) `ZINC000151975008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000151975008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000151975008 none CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 28, 42, 28, 28, 28, 10, 28, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 28, 42, 42, 42, 28, 28, 28, 28, 6, 5, 5, 5, 5, 5, 5, 5, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000151975008 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 Building ZINC000151975008 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000151975008 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 142) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)C1) `ZINC000151975008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000151975008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000151975008 none CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 29, 41, 29, 29, 29, 11, 29, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 41, 41, 41, 29, 29, 29, 29, 6, 5, 5, 5, 5, 5, 5, 5, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 143) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)C1) `ZINC000151975008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000151975008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000151975008 none CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 28, 42, 28, 28, 28, 10, 28, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 28, 42, 42, 42, 28, 28, 28, 28, 6, 5, 5, 5, 5, 5, 5, 5, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000151975008 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975008 Building ZINC000151975095 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000151975095 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/144 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)C1) `ZINC000151975095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000151975095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000151975095 none CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 28, 42, 28, 28, 28, 8, 28, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 28, 42, 42, 42, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/145 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)C1) `ZINC000151975095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000151975095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000151975095 none CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 28, 41, 28, 28, 28, 10, 28, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 28, 41, 41, 41, 28, 28, 28, 28, 6, 5, 5, 5, 5, 5, 5, 5, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000151975095 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 Building ZINC000151975095 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000151975095 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 144) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)C1) `ZINC000151975095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000151975095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000151975095 none CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 28, 42, 28, 28, 28, 8, 28, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 28, 42, 42, 42, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 145) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)C1) `ZINC000151975095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000151975095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000151975095 none CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 28, 41, 28, 28, 28, 10, 28, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 28, 41, 41, 41, 28, 28, 28, 28, 6, 5, 5, 5, 5, 5, 5, 5, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000151975095 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000151975095 Building ZINC000408038252 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408038252 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/146 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CO)CC1) `ZINC000408038252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408038252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408038252 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 9, 19, 19, 19, 19, 37, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 37, 37, 111, 19, 19, 19, 19] 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]) total number of confs: 239 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/147 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CO)CC1) `ZINC000408038252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408038252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408038252 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 9, 20, 20, 20, 20, 41, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 41, 41, 123, 20, 20, 20, 20] 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]) total number of confs: 265 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408038252 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 Building ZINC000408038252 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408038252 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 146) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CO)CC1) `ZINC000408038252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408038252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408038252 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 9, 19, 19, 19, 19, 37, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 37, 37, 111, 19, 19, 19, 19] 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]) total number of confs: 239 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 147) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CO)CC1) `ZINC000408038252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408038252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408038252 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 9, 20, 20, 20, 20, 41, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 41, 41, 123, 20, 20, 20, 20] 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]) total number of confs: 265 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408038252 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408038252 Building ZINC000613665168 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613665168 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/148 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000613665168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613665168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000613665168 none CN(C)[C@@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 36, 23, 23, 23, 23, 23, 11, 23, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 7, 8, 8, 8, 8, 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]) total number of confs: 113 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/149 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000613665168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613665168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000613665168 none CN(C)[C@@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 9, 25, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 5, 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]) total number of confs: 114 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613665168 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 Building ZINC000613665168 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613665168 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 148) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000613665168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613665168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000613665168 none CN(C)[C@@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 36, 23, 23, 23, 23, 23, 11, 23, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 7, 8, 8, 8, 8, 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]) total number of confs: 113 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 149) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000613665168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613665168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000613665168 none CN(C)[C@@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 9, 25, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 5, 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]) total number of confs: 114 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613665168 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613665168 Building ZINC000362588943 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362588943 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/150 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCCC1) `ZINC000362588943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362588943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000362588943 none COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 15, 41, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 41, 41, 41, 6, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/151 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCCC1) `ZINC000362588943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362588943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000362588943 none COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 16, 41, 7, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 16, 41, 41, 41, 7, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362588943 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 Building ZINC000362588943 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362588943 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 150) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCCC1) `ZINC000362588943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362588943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000362588943 none COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 15, 41, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 41, 41, 41, 6, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 151) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCCC1) `ZINC000362588943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362588943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000362588943 none COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 16, 41, 7, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 16, 41, 41, 41, 7, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362588943 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362588943 Building ZINC000167682141 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167682141 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/152 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/152' -> `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)N1CCO[C@H](C)[C@H]1C) `ZINC000167682141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167682141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682141 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 24 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/153 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/153' -> `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)N1CCO[C@H](C)[C@H]1C) `ZINC000167682141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167682141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682141 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 20 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167682141 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 Building ZINC000167682141 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167682141 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 152) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@H]1C) `ZINC000167682141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167682141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682141 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 24 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 153) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@H]1C) `ZINC000167682141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167682141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682141 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 20 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167682141 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682141 Building ZINC000647673330 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647673330 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/154 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000647673330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647673330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647673330 none CC[C@H](C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 14, 10, 14, 14, 6, 2, 6, 6, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 16, 16, 16, 16, 16, 14, 14, 14, 10, 10, 13, 13, 39, 2, 6, 15, 15, 15, 15, 15, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 206 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/155 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000647673330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647673330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647673330 none CC[C@H](C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 14, 10, 14, 14, 6, 2, 6, 6, 10, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 6, 16, 16, 16, 16, 16, 14, 14, 14, 10, 10, 10, 10, 30, 2, 6, 14, 14, 14, 14, 14, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647673330 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 Building ZINC000647673330 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647673330 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 154) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@H](C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000647673330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647673330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647673330 none CC[C@H](C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 14, 10, 14, 14, 6, 2, 6, 6, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 16, 16, 16, 16, 16, 14, 14, 14, 10, 10, 13, 13, 39, 2, 6, 15, 15, 15, 15, 15, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 206 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 155) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@H](C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000647673330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647673330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647673330 none CC[C@H](C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 14, 10, 14, 14, 6, 2, 6, 6, 10, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 6, 16, 16, 16, 16, 16, 14, 14, 14, 10, 10, 10, 10, 30, 2, 6, 14, 14, 14, 14, 14, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647673330 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673330 Building ZINC000647673333 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647673333 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/156 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000647673333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647673333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647673333 none CC[C@@H](C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 12, 15, 15, 8, 2, 8, 8, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 13, 13, 39, 2, 6, 18, 18, 18, 18, 18, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/157 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000647673333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647673333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647673333 none CC[C@@H](C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 13, 16, 16, 8, 2, 8, 8, 14, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 16, 16, 16, 16, 16, 16, 16, 16, 13, 13, 14, 14, 42, 2, 6, 15, 15, 15, 15, 15, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647673333 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 Building ZINC000647673333 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647673333 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 156) grep: /scratch/xiaobo/170854/xdl-8058088.90/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@@H](C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000647673333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647673333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647673333 none CC[C@@H](C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 12, 15, 15, 8, 2, 8, 8, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 13, 13, 39, 2, 6, 18, 18, 18, 18, 18, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 157) grep: /scratch/xiaobo/170854/xdl-8058088.90/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@@H](C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000647673333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647673333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647673333 none CC[C@@H](C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 13, 16, 16, 8, 2, 8, 8, 14, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 16, 16, 16, 16, 16, 16, 16, 16, 13, 13, 14, 14, 42, 2, 6, 15, 15, 15, 15, 15, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647673333 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647673333 Building ZINC000167543388 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167543388 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/158 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C)OCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000167543388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167543388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000167543388 none C[C@@H]1[C@H](C)OCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 2, 14, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 40 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]) total number of confs: 48 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/159 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C)OCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000167543388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167543388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000167543388 none C[C@@H]1[C@H](C)OCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 13, 2, 13, 1, 1, 1, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12] 44 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]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167543388 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 Building ZINC000167543388 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167543388 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 158) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C)OCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000167543388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167543388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000167543388 none C[C@@H]1[C@H](C)OCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 2, 14, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 40 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]) total number of confs: 48 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 159) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C)OCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000167543388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167543388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000167543388 none C[C@@H]1[C@H](C)OCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 13, 2, 13, 1, 1, 1, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12] 44 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]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167543388 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543388 Building ZINC000167543503 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167543503 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/160 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000167543503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167543503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543503 none C[C@@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 17, 3, 17, 1, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/161 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000167543503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167543503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543503 none C[C@@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 16, 2, 16, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 10, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167543503 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 Building ZINC000167543503 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167543503 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 160) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000167543503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167543503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543503 none C[C@@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 17, 3, 17, 1, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 161) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000167543503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167543503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543503 none C[C@@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 16, 2, 16, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 10, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167543503 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543503 Building ZINC000167543610 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167543610 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/162 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C) `ZINC000167543610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167543610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543610 none C[C@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 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: [20, 20, 20, 20, 20, 20, 15, 2, 15, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/163 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C) `ZINC000167543610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167543610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543610 none C[C@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 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: [20, 20, 20, 20, 20, 20, 14, 3, 14, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167543610 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 Building ZINC000167543610 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167543610 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 162) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C) `ZINC000167543610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167543610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543610 none C[C@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 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: [20, 20, 20, 20, 20, 20, 15, 2, 15, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 163) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C) `ZINC000167543610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167543610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543610 none C[C@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 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: [20, 20, 20, 20, 20, 20, 14, 3, 14, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167543610 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543610 Building ZINC000167543715 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167543715 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/164 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000167543715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167543715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543715 none C[C@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 12, 2, 12, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 17, 17, 17] 48 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 48 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/165 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000167543715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167543715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543715 none C[C@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 15, 2, 15, 1, 1, 1, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 12, 12, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167543715 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 Building ZINC000167543715 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167543715 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 164) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000167543715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167543715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543715 none C[C@H]1OCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 12, 2, 12, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 17, 17, 17] 48 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 48 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 165) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000167543715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167543715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000167543715 none C[C@H]1OCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 15, 2, 15, 1, 1, 1, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 12, 12, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167543715 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167543715 Building ZINC000584529140 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584529140 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/166 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN) `ZINC000584529140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529140 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 19, 19, 33, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 19, 19, 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]) total number of confs: 121 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/167 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN) `ZINC000584529140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529140 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 10, 2, 13, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 21, 21, 31, 31, 31, 31] 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]) total number of confs: 103 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584529140 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 Building ZINC000584529140 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584529140 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 166) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN) `ZINC000584529140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529140 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 19, 19, 33, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 19, 19, 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]) total number of confs: 121 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 167) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN) `ZINC000584529140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529140 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 10, 2, 13, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 21, 21, 31, 31, 31, 31] 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]) total number of confs: 103 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584529140 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529140 Building ZINC000584529141 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584529141 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/168 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN) `ZINC000584529141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529141 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 12, 2, 12, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 32, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 20, 20, 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]) total number of confs: 112 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/169 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN) `ZINC000584529141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529141 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 10, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 29, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 17, 17, 29, 29, 29, 29] 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]) total number of confs: 103 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584529141 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 Building ZINC000584529141 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584529141 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 168) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN) `ZINC000584529141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529141 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 12, 2, 12, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 32, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 20, 20, 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]) total number of confs: 112 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 169) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN) `ZINC000584529141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529141 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 10, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 29, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 17, 17, 29, 29, 29, 29] 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]) total number of confs: 103 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584529141 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529141 Building ZINC000584529142 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584529142 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/170 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN) `ZINC000584529142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584529142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529142 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 12, 2, 11, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 29, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 20, 20, 29, 29, 29, 29] 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]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/171 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN) `ZINC000584529142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584529142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529142 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 13, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 21, 21, 31, 31, 31, 31] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584529142 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 Building ZINC000584529142 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584529142 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 170) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN) `ZINC000584529142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584529142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529142 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 12, 2, 11, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 29, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 20, 20, 29, 29, 29, 29] 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]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 171) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN) `ZINC000584529142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584529142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529142 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 13, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 21, 21, 31, 31, 31, 31] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584529142 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529142 Building ZINC000584529143 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584529143 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/172 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN) `ZINC000584529143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584529143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529143 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 11, 2, 12, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 32, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 20, 20, 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]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/173 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN) `ZINC000584529143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584529143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529143 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 18, 18, 30, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 18, 18, 30, 30, 30, 30] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584529143 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 Building ZINC000584529143 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584529143 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 172) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN) `ZINC000584529143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584529143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529143 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 11, 2, 12, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 32, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 20, 20, 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]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 173) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN) `ZINC000584529143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584529143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000584529143 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1CN 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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 18, 18, 30, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 18, 18, 30, 30, 30, 30] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584529143 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584529143 Building ZINC000174453856 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174453856 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/174 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000174453856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174453856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000174453856 none CC(C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [29, 24, 30, 15, 23, 24, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 29, 30, 30, 30, 30, 24, 24, 24, 72, 15, 15, 4, 8, 8, 8, 8, 8] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 223 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/175 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000174453856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174453856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000174453856 none CC(C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [27, 24, 27, 12, 25, 26, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 25, 27, 27, 27, 26, 26, 26, 78, 12, 12, 2, 7, 7, 7, 7, 7] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 212 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000174453856 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 Building ZINC000174453856 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174453856 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 174) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000174453856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174453856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000174453856 none CC(C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [29, 24, 30, 15, 23, 24, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 29, 30, 30, 30, 30, 24, 24, 24, 72, 15, 15, 4, 8, 8, 8, 8, 8] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 223 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 175) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000174453856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174453856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000174453856 none CC(C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [27, 24, 27, 12, 25, 26, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 25, 27, 27, 27, 26, 26, 26, 78, 12, 12, 2, 7, 7, 7, 7, 7] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 212 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000174453856 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453856 Building ZINC000174453875 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174453875 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/176 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000174453875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174453875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000174453875 none CC(C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [27, 23, 27, 12, 25, 26, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 24, 27, 27, 27, 26, 26, 26, 78, 12, 12, 2, 7, 7, 7, 7, 7] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 215 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/177 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000174453875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174453875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000174453875 none CC(C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [29, 25, 29, 15, 22, 25, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 25, 25, 25, 75, 15, 15, 4, 8, 8, 8, 8, 8] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000174453875 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 Building ZINC000174453875 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174453875 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 176) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000174453875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174453875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000174453875 none CC(C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [27, 23, 27, 12, 25, 26, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 24, 27, 27, 27, 26, 26, 26, 78, 12, 12, 2, 7, 7, 7, 7, 7] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 215 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 177) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000174453875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174453875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000174453875 none CC(C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [29, 25, 29, 15, 22, 25, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 25, 25, 25, 75, 15, 15, 4, 8, 8, 8, 8, 8] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000174453875 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000174453875 Building ZINC000909322444 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909322444 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/178 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)NCCN1CCCCC1) `ZINC000909322444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909322444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000909322444 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)NCCN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 17, 43, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 43, 43, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/179 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)NCCN1CCCCC1) `ZINC000909322444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909322444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000909322444 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)NCCN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 17, 43, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 43, 43, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000909322444 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 Building ZINC000909322444 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909322444 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 178) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)NCCN1CCCCC1) `ZINC000909322444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909322444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000909322444 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)NCCN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 17, 43, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 43, 43, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 179) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)NCCN1CCCCC1) `ZINC000909322444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909322444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000909322444 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)NCCN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 17, 43, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 43, 43, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000909322444 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909322444 Building ZINC000362733684 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362733684 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/180 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362733684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733684 none CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 31, 12, 31, 30, 4, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 24, 24, 24, 35, 35, 35, 35, 35, 31, 31, 31, 4, 5, 5, 5, 5, 5, 5, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/181 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362733684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733684 none CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 10, 28, 26, 4, 10, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 10, 21, 21, 21, 33, 33, 33, 32, 33, 28, 28, 28, 4, 5, 5, 5, 5, 5, 5, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362733684 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 Building ZINC000362733684 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362733684 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 180) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362733684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733684 none CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 31, 12, 31, 30, 4, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 24, 24, 24, 35, 35, 35, 35, 35, 31, 31, 31, 4, 5, 5, 5, 5, 5, 5, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 181) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362733684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733684 none CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 10, 28, 26, 4, 10, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 10, 21, 21, 21, 33, 33, 33, 32, 33, 28, 28, 28, 4, 5, 5, 5, 5, 5, 5, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362733684 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733684 Building ZINC000362733685 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362733685 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/182 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362733685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733685 none CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 31, 13, 33, 32, 4, 13, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 13, 24, 24, 24, 37, 37, 37, 37, 36, 33, 33, 33, 4, 5, 5, 5, 5, 5, 5, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 209 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/183 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362733685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733685 none CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 31, 12, 32, 32, 4, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 25, 25, 25, 36, 36, 36, 35, 36, 32, 32, 32, 4, 5, 5, 5, 5, 5, 5, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362733685 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 Building ZINC000362733685 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362733685 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 182) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362733685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733685 none CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 31, 13, 33, 32, 4, 13, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 13, 24, 24, 24, 37, 37, 37, 37, 36, 33, 33, 33, 4, 5, 5, 5, 5, 5, 5, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 209 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 183) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362733685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733685 none CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 31, 12, 32, 32, 4, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 25, 25, 25, 36, 36, 36, 35, 36, 32, 32, 32, 4, 5, 5, 5, 5, 5, 5, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362733685 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733685 Building ZINC000362733686 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362733686 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/184 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362733686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733686 none CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 31, 12, 32, 32, 4, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 25, 25, 25, 36, 36, 36, 35, 36, 32, 32, 32, 4, 5, 5, 5, 5, 5, 5, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/185 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362733686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733686 none CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 31, 13, 33, 32, 4, 13, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 13, 24, 24, 24, 37, 37, 37, 36, 37, 33, 33, 33, 4, 5, 5, 5, 5, 5, 5, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 209 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362733686 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 Building ZINC000362733686 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362733686 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 184) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362733686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733686 none CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 31, 12, 32, 32, 4, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 25, 25, 25, 36, 36, 36, 35, 36, 32, 32, 32, 4, 5, 5, 5, 5, 5, 5, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 185) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC) `ZINC000362733686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362733686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362733686 none CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 31, 13, 33, 32, 4, 13, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 13, 24, 24, 24, 37, 37, 37, 36, 37, 33, 33, 33, 4, 5, 5, 5, 5, 5, 5, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 209 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362733686 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362733686 Building ZINC000377510851 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377510851 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/186 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC(F)(F)C2)cn1) `ZINC000377510851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377510851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000377510851 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 15, 15, 5, 1, 8, 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, 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: [14, 4, 4, 4, 1, 1, 1, 2, 8, 12, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 14, 14, 14, 14, 14, 4, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/187 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCOCC(F)(F)C2)cn1) `ZINC000377510851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377510851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000377510851 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCOCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 15, 15, 5, 1, 8, 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, 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: [19, 5, 5, 5, 1, 1, 1, 2, 8, 13, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 19, 19, 19, 19, 19, 5, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000377510851 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 Building ZINC000377510851 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377510851 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 186) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC(F)(F)C2)cn1) `ZINC000377510851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377510851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000377510851 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 15, 15, 5, 1, 8, 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, 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: [14, 4, 4, 4, 1, 1, 1, 2, 8, 12, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 14, 14, 14, 14, 14, 4, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 187) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCOCC(F)(F)C2)cn1) `ZINC000377510851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377510851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000377510851 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCOCC(F)(F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 15, 15, 5, 1, 8, 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, 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: [19, 5, 5, 5, 1, 1, 1, 2, 8, 13, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 19, 19, 19, 19, 19, 5, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000377510851 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377510851 Building ZINC000362764935 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362764935 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/188 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000362764935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362764935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000362764935 none CCOC(=O)[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 9, 6, 8, 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, 34, 33, 11, 33, 6, 11, 11, 3, 6, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 11, 11, 11, 6, 6, 6, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/189 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000362764935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362764935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000362764935 none CCOC(=O)[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 9, 6, 8, 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: [42, 38, 36, 12, 36, 7, 12, 12, 5, 7, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 42, 42, 42, 42, 42, 12, 12, 12, 7, 7, 7, 5, 5, 5, 5, 5, 5] 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362764935 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 Building ZINC000362764935 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362764935 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 188) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCOC(=O)[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000362764935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362764935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000362764935 none CCOC(=O)[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 9, 6, 8, 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, 34, 33, 11, 33, 6, 11, 11, 3, 6, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 11, 11, 11, 6, 6, 6, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 189) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCOC(=O)[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000362764935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362764935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000362764935 none CCOC(=O)[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 9, 6, 8, 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: [42, 38, 36, 12, 36, 7, 12, 12, 5, 7, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 42, 42, 42, 42, 42, 12, 12, 12, 7, 7, 7, 5, 5, 5, 5, 5, 5] 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362764935 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362764935 Building ZINC000167681933 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167681933 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/190 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/190' -> `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)N1CCO[C@H](C)[C@@H]1C) `ZINC000167681933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167681933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167681933 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 20 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 39 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/191 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/191' -> `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)N1CCO[C@H](C)[C@@H]1C) `ZINC000167681933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167681933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167681933 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 23 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 40 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167681933 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 Building ZINC000167681933 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167681933 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 190) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@@H]1C) `ZINC000167681933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167681933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167681933 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 20 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 39 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 191) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@@H]1C) `ZINC000167681933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167681933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167681933 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 23 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 40 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167681933 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167681933 Building ZINC000362875991 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362875991 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/192 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC000362875991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362875991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000362875991 none Cn1nnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 18, 18, 4, 3, 3, 3, 3] 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/193 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC000362875991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362875991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000362875991 none Cn1nnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 18, 18, 4, 3, 3, 3, 3] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362875991 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 Building ZINC000362875991 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362875991 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 192) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1nnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC000362875991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362875991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000362875991 none Cn1nnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 18, 18, 4, 3, 3, 3, 3] 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 193) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1nnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC000362875991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362875991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000362875991 none Cn1nnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 18, 18, 4, 3, 3, 3, 3] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362875991 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362875991 Building ZINC000167682036 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167682036 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/194 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/194' -> `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)N1CCO[C@@H](C)[C@@H]1C) `ZINC000167682036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167682036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682036 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 26 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/195 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/195' -> `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)N1CCO[C@@H](C)[C@@H]1C) `ZINC000167682036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167682036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682036 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167682036 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 Building ZINC000167682036 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167682036 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 194) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@@H]1C) `ZINC000167682036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167682036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682036 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 26 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 195) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@@H]1C) `ZINC000167682036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167682036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682036 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167682036 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682036 Building ZINC000167682246 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167682246 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/196 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/196' -> `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)N1CCO[C@@H](C)[C@H]1C) `ZINC000167682246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167682246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682246 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 15 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/197 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/197' -> `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)N1CCO[C@@H](C)[C@H]1C) `ZINC000167682246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167682246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682246 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 16 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 28 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167682246 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 Building ZINC000167682246 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000167682246 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 196) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@H]1C) `ZINC000167682246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000167682246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682246 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 15 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 197) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@H]1C) `ZINC000167682246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000167682246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000167682246 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 16 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 28 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000167682246 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000167682246 Building ZINC000362956734 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362956734 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/198 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)C1(C(N)=O)CCCC1) `ZINC000362956734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362956734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000362956734 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)C1(C(N)=O)CCCC1 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', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 15, 30, 43, 43, 30, 30, 30, 30, 10, 10, 10, 6, 6, 6, 6, 6, 6, 43, 43, 30, 30, 30, 30, 30, 30, 30, 30] 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: 135 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/199 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)C1(C(N)=O)CCCC1) `ZINC000362956734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362956734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000362956734 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)C1(C(N)=O)CCCC1 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', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 13, 28, 41, 41, 28, 28, 28, 28, 8, 8, 8, 6, 6, 6, 6, 6, 6, 41, 41, 28, 28, 28, 28, 28, 28, 28, 28] 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: 128 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362956734 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 Building ZINC000362956734 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362956734 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 198) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)C1(C(N)=O)CCCC1) `ZINC000362956734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362956734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000362956734 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)C1(C(N)=O)CCCC1 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', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 15, 30, 43, 43, 30, 30, 30, 30, 10, 10, 10, 6, 6, 6, 6, 6, 6, 43, 43, 30, 30, 30, 30, 30, 30, 30, 30] 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: 135 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 199) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)C1(C(N)=O)CCCC1) `ZINC000362956734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362956734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000362956734 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)C1(C(N)=O)CCCC1 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', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 13, 28, 41, 41, 28, 28, 28, 28, 8, 8, 8, 6, 6, 6, 6, 6, 6, 41, 41, 28, 28, 28, 28, 28, 28, 28, 28] 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: 128 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000362956734 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000362956734 Building ZINC000516662423 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516662423 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/200 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C2CC2)C(C)(C)CO)cn1) `ZINC000516662423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516662423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000516662423 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C2CC2)C(C)(C)CO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 11, 10, 11, 11, 6, 6, 14, 14, 14, 14, 14, 6, 2, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 33, 6] 150 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: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/201 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C2CC2)C(C)(C)CO)cn1) `ZINC000516662423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516662423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000516662423 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C2CC2)C(C)(C)CO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 13, 12, 13, 14, 7, 7, 17, 17, 17, 17, 17, 7, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 14, 14, 42, 7] 150 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000516662423 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 Building ZINC000516662423 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516662423 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 200) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C2CC2)C(C)(C)CO)cn1) `ZINC000516662423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516662423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000516662423 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C2CC2)C(C)(C)CO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 11, 10, 11, 11, 6, 6, 14, 14, 14, 14, 14, 6, 2, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 33, 6] 150 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: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 201) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C2CC2)C(C)(C)CO)cn1) `ZINC000516662423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516662423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000516662423 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C2CC2)C(C)(C)CO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 13, 12, 13, 14, 7, 7, 17, 17, 17, 17, 17, 7, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 14, 14, 42, 7] 150 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000516662423 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000516662423 Building ZINC000377713194 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377713194 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/202 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCOC(C)(C)C2)cn1) `ZINC000377713194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377713194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000377713194 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCOC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 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] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 15, 21, 26, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/203 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCOC(C)(C)C2)cn1) `ZINC000377713194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377713194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000377713194 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCOC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 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] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 14, 19, 25, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000377713194 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 Building ZINC000377713194 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377713194 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 202) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCOC(C)(C)C2)cn1) `ZINC000377713194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377713194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000377713194 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCOC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 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] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 15, 21, 26, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 203) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCOC(C)(C)C2)cn1) `ZINC000377713194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377713194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000377713194 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCOC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 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] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 14, 19, 25, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000377713194 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000377713194 Building ZINC000278818691 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278818691 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/204 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cc1) `ZINC000278818691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278818691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818691 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 26, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 138, 46, 46, 46, 46, 46, 46, 46, 4, 4] 150 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]) total number of confs: 290 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/205 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cc1) `ZINC000278818691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278818691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818691 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 31, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 141, 47, 47, 47, 47, 47, 47, 47, 5, 5] 150 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]) total number of confs: 304 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000278818691 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 Building ZINC000278818691 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278818691 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 204) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cc1) `ZINC000278818691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278818691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818691 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 26, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 138, 46, 46, 46, 46, 46, 46, 46, 4, 4] 150 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]) total number of confs: 290 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 205) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cc1) `ZINC000278818691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278818691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818691 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 31, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 141, 47, 47, 47, 47, 47, 47, 47, 5, 5] 150 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]) total number of confs: 304 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000278818691 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818691 Building ZINC000278818710 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278818710 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/206 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cc1) `ZINC000278818710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278818710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818710 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 129, 43, 43, 43, 43, 43, 43, 43, 4, 4] 150 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]) total number of confs: 286 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/207 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cc1) `ZINC000278818710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278818710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818710 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 30, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 18, 18, 132, 44, 44, 44, 44, 44, 44, 44, 4, 4] 150 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]) total number of confs: 279 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000278818710 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 Building ZINC000278818710 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278818710 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 206) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cc1) `ZINC000278818710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278818710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818710 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 129, 43, 43, 43, 43, 43, 43, 43, 4, 4] 150 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]) total number of confs: 286 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 207) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cc1) `ZINC000278818710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278818710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818710 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 30, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 18, 18, 132, 44, 44, 44, 44, 44, 44, 44, 4, 4] 150 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]) total number of confs: 279 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000278818710 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818710 Building ZINC000278818727 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278818727 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/208 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cc1) `ZINC000278818727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278818727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818727 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 30, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 132, 44, 44, 44, 44, 44, 44, 44, 5, 5] 150 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]) total number of confs: 299 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/209 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cc1) `ZINC000278818727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278818727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818727 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 129, 43, 43, 43, 43, 43, 43, 43, 4, 4] 150 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]) total number of confs: 286 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000278818727 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 Building ZINC000278818727 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278818727 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 208) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cc1) `ZINC000278818727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278818727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818727 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 30, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 132, 44, 44, 44, 44, 44, 44, 44, 5, 5] 150 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]) total number of confs: 299 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 209) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cc1) `ZINC000278818727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278818727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818727 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 129, 43, 43, 43, 43, 43, 43, 43, 4, 4] 150 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]) total number of confs: 286 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000278818727 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818727 Building ZINC000278818738 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278818738 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/210 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cc1) `ZINC000278818738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278818738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818738 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 31, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 5, 19, 19, 141, 47, 47, 47, 47, 47, 47, 47, 4, 4] 150 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]) total number of confs: 299 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/211 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cc1) `ZINC000278818738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278818738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818738 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 26, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 138, 46, 46, 46, 46, 46, 46, 46, 4, 4] 150 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]) total number of confs: 292 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000278818738 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 Building ZINC000278818738 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278818738 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 210) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cc1) `ZINC000278818738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278818738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818738 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 31, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 5, 19, 19, 141, 47, 47, 47, 47, 47, 47, 47, 4, 4] 150 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]) total number of confs: 299 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 211) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cc1) `ZINC000278818738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278818738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000278818738 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 26, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 138, 46, 46, 46, 46, 46, 46, 46, 4, 4] 150 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]) total number of confs: 292 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000278818738 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000278818738 Building ZINC000497153787 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497153787 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/212 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C(C)C)CC1) `ZINC000497153787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497153787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000497153787 none CCOC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C(C)C)CC1 NO_LONG_NAME dock atom types: ['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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need 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, 40, 27, 40, 27, 27, 27, 6, 3, 1, 3, 1, 1, 1, 2, 2, 27, 27, 50, 50, 50, 50, 50, 27, 27, 27, 27, 25, 3, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/213 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C(C)C)CC1) `ZINC000497153787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497153787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000497153787 none CCOC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C(C)C)CC1 NO_LONG_NAME dock atom types: ['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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need 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, 26, 42, 26, 26, 26, 6, 3, 1, 3, 1, 1, 1, 2, 2, 26, 26, 50, 50, 50, 50, 50, 26, 26, 26, 26, 24, 3, 2, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000497153787 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 Building ZINC000497153787 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497153787 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 212) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCOC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C(C)C)CC1) `ZINC000497153787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497153787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000497153787 none CCOC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C(C)C)CC1 NO_LONG_NAME dock atom types: ['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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need 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, 40, 27, 40, 27, 27, 27, 6, 3, 1, 3, 1, 1, 1, 2, 2, 27, 27, 50, 50, 50, 50, 50, 27, 27, 27, 27, 25, 3, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 213) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCOC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C(C)C)CC1) `ZINC000497153787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497153787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000497153787 none CCOC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C(C)C)CC1 NO_LONG_NAME dock atom types: ['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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need 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, 26, 42, 26, 26, 26, 6, 3, 1, 3, 1, 1, 1, 2, 2, 26, 26, 50, 50, 50, 50, 50, 26, 26, 26, 26, 24, 3, 2, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000497153787 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497153787 Building ZINC000177220658 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177220658 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/214 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177220658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177220658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000177220658 none COC(=O)[C@@]1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 9, 6, 8, 10, 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: [30, 30, 12, 30, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 30, 30, 30, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/215 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177220658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177220658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000177220658 none COC(=O)[C@@]1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 9, 6, 8, 10, 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: [33, 33, 14, 33, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 14, 33, 33, 33, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 14, 14] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000177220658 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 Building ZINC000177220658 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177220658 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 214) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC(=O)[C@@]1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177220658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177220658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000177220658 none COC(=O)[C@@]1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 9, 6, 8, 10, 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: [30, 30, 12, 30, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 30, 30, 30, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 215) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC(=O)[C@@]1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177220658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177220658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000177220658 none COC(=O)[C@@]1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 9, 6, 8, 10, 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: [33, 33, 14, 33, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 14, 33, 33, 33, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 14, 14] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000177220658 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220658 Building ZINC000177220676 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177220676 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/216 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177220676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177220676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000177220676 none COC(=O)[C@]1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 14, 34, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 14, 34, 34, 34, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 14, 14] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/217 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177220676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177220676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000177220676 none COC(=O)[C@]1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 9, 6, 8, 10, 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: [31, 31, 13, 31, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 13, 31, 31, 31, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000177220676 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 Building ZINC000177220676 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177220676 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 216) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177220676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177220676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000177220676 none COC(=O)[C@]1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 14, 34, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 14, 34, 34, 34, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 14, 14] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 217) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177220676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177220676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000177220676 none COC(=O)[C@]1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 9, 6, 8, 10, 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: [31, 31, 13, 31, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 13, 31, 31, 31, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000177220676 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177220676 Building ZINC000270984610 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270984610 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/218 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)C)cn1) `ZINC000270984610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270984610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000270984610 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 9, 9, 15, 9, 10, 10, 10, 7, 7, 21, 21, 21, 21, 21, 7, 3, 15, 15, 45, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/219 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)C)cn1) `ZINC000270984610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270984610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000270984610 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 10, 10, 15, 10, 10, 10, 10, 7, 7, 20, 20, 20, 20, 20, 7, 4, 15, 15, 45, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000270984610 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 Building ZINC000270984610 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270984610 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 218) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)C)cn1) `ZINC000270984610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270984610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000270984610 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 9, 9, 15, 9, 10, 10, 10, 7, 7, 21, 21, 21, 21, 21, 7, 3, 15, 15, 45, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 219) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)C)cn1) `ZINC000270984610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270984610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000270984610 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 10, 10, 15, 10, 10, 10, 10, 7, 7, 20, 20, 20, 20, 20, 7, 4, 15, 15, 45, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000270984610 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984610 Building ZINC000270984612 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270984612 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/220 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)C)cn1) `ZINC000270984612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270984612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000270984612 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 14, 8, 12, 12, 12, 6, 6, 17, 17, 17, 17, 17, 6, 3, 14, 14, 42, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 172 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/221 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)C)cn1) `ZINC000270984612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270984612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000270984612 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 18, 10, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 3, 18, 18, 54, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000270984612 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 Building ZINC000270984612 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270984612 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 220) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)C)cn1) `ZINC000270984612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270984612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000270984612 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 14, 8, 12, 12, 12, 6, 6, 17, 17, 17, 17, 17, 6, 3, 14, 14, 42, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 172 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 221) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)C)cn1) `ZINC000270984612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270984612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000270984612 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 18, 10, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 3, 18, 18, 54, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000270984612 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000270984612 Building ZINC000177524376 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177524376 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/222 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177524376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177524376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000177524376 none CN(C)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 31, 15, 15, 15, 15, 15, 4, 15, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 15, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 4, 9, 9, 9, 9, 9, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/223 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177524376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177524376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000177524376 none CN(C)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 32, 13, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 13, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 13, 13, 4, 10, 10, 10, 10, 10, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000177524376 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 Building ZINC000177524376 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177524376 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 222) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(C)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177524376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177524376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000177524376 none CN(C)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 31, 15, 15, 15, 15, 15, 4, 15, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 15, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 4, 9, 9, 9, 9, 9, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 223) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(C)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000177524376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177524376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000177524376 none CN(C)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 32, 13, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 13, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 13, 13, 4, 10, 10, 10, 10, 10, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000177524376 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000177524376 Building ZINC000678092227 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000678092227 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/224 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CO)CCC2)cn1) `ZINC000678092227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000678092227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000678092227 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CO)CCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 4, 4, 6, 10, 21, 10, 10, 10, 8, 8, 26, 26, 26, 26, 26, 8, 4, 21, 21, 59, 10, 10, 10, 10, 10, 10, 8] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 216 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/225 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CO)CCC2)cn1) `ZINC000678092227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000678092227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000678092227 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CO)CCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 11, 21, 11, 11, 11, 7, 7, 24, 24, 24, 24, 24, 7, 4, 21, 21, 61, 11, 11, 11, 11, 11, 11, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 211 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000678092227 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 Building ZINC000678092227 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000678092227 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 224) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CO)CCC2)cn1) `ZINC000678092227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000678092227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000678092227 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CO)CCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 4, 4, 6, 10, 21, 10, 10, 10, 8, 8, 26, 26, 26, 26, 26, 8, 4, 21, 21, 59, 10, 10, 10, 10, 10, 10, 8] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 216 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 225) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CO)CCC2)cn1) `ZINC000678092227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000678092227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000678092227 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CO)CCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 11, 21, 11, 11, 11, 7, 7, 24, 24, 24, 24, 24, 7, 4, 21, 21, 61, 11, 11, 11, 11, 11, 11, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 211 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000678092227 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000678092227 Building ZINC000378016041 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378016041 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/226 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](CO)(C(C)C)C2)cn1) `ZINC000378016041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378016041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000378016041 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](CO)(C(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 2, 2, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 16, 6, 13, 13, 6, 2, 2, 8, 8, 8, 8, 8, 2, 6, 6, 6, 6, 16, 16, 48, 13, 13, 13, 13, 13, 13, 13, 6, 6, 2] 150 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: 160 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/227 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](CO)(C(C)C)C2)cn1) `ZINC000378016041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378016041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000378016041 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](CO)(C(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 4, 4, 4, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 15, 5, 10, 10, 5, 4, 4, 17, 17, 17, 17, 17, 4, 5, 5, 5, 5, 15, 15, 45, 10, 10, 10, 10, 10, 10, 10, 5, 5, 4] 150 rigid atoms, others: [8, 4, 5, 6, 7] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 170 number of broken/clashed sets: 146 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378016041 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 Building ZINC000378016041 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378016041 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 226) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](CO)(C(C)C)C2)cn1) `ZINC000378016041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378016041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000378016041 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](CO)(C(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 2, 2, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 16, 6, 13, 13, 6, 2, 2, 8, 8, 8, 8, 8, 2, 6, 6, 6, 6, 16, 16, 48, 13, 13, 13, 13, 13, 13, 13, 6, 6, 2] 150 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: 160 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 227) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](CO)(C(C)C)C2)cn1) `ZINC000378016041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378016041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000378016041 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](CO)(C(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 4, 4, 4, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 15, 5, 10, 10, 5, 4, 4, 17, 17, 17, 17, 17, 4, 5, 5, 5, 5, 15, 15, 45, 10, 10, 10, 10, 10, 10, 10, 5, 5, 4] 150 rigid atoms, others: [8, 4, 5, 6, 7] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 170 number of broken/clashed sets: 146 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378016041 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016041 Building ZINC000378016042 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378016042 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/228 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](CO)(C(C)C)C2)cn1) `ZINC000378016042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378016042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000378016042 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](CO)(C(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 4, 4, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 14, 5, 10, 10, 5, 4, 4, 16, 16, 16, 16, 16, 4, 5, 5, 5, 5, 14, 14, 42, 10, 10, 10, 10, 10, 10, 10, 5, 5, 4] 150 rigid atoms, others: [8, 4, 5, 6, 7] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 161 number of broken/clashed sets: 148 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/229 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](CO)(C(C)C)C2)cn1) `ZINC000378016042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378016042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000378016042 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](CO)(C(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 2, 2, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 16, 6, 13, 13, 6, 2, 2, 8, 8, 8, 8, 8, 2, 6, 6, 6, 6, 16, 16, 48, 13, 13, 13, 13, 13, 13, 13, 6, 6, 2] 150 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: 160 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378016042 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 Building ZINC000378016042 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378016042 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 228) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](CO)(C(C)C)C2)cn1) `ZINC000378016042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378016042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000378016042 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](CO)(C(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 4, 4, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 14, 5, 10, 10, 5, 4, 4, 16, 16, 16, 16, 16, 4, 5, 5, 5, 5, 14, 14, 42, 10, 10, 10, 10, 10, 10, 10, 5, 5, 4] 150 rigid atoms, others: [8, 4, 5, 6, 7] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 161 number of broken/clashed sets: 148 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 229) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](CO)(C(C)C)C2)cn1) `ZINC000378016042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378016042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000378016042 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](CO)(C(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 2, 2, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 16, 6, 13, 13, 6, 2, 2, 8, 8, 8, 8, 8, 2, 6, 6, 6, 6, 16, 16, 48, 13, 13, 13, 13, 13, 13, 13, 6, 6, 2] 150 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: 160 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378016042 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378016042 Building ZINC000179261199 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179261199 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/230 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](CO)CC2)cn1) `ZINC000179261199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179261199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000179261199 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 12, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 16, 10, 10, 6, 6, 15, 15, 15, 15, 15, 6, 2, 10, 10, 10, 10, 16, 16, 48, 10, 10, 10, 10, 6] 150 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/231 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](CO)CC2)cn1) `ZINC000179261199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179261199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000179261199 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 12, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 18, 11, 11, 6, 6, 16, 16, 16, 16, 16, 6, 3, 11, 11, 11, 11, 18, 18, 54, 11, 11, 11, 11, 6] 150 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000179261199 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 Building ZINC000179261199 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179261199 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 230) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](CO)CC2)cn1) `ZINC000179261199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179261199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000179261199 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 12, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 16, 10, 10, 6, 6, 15, 15, 15, 15, 15, 6, 2, 10, 10, 10, 10, 16, 16, 48, 10, 10, 10, 10, 6] 150 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 231) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](CO)CC2)cn1) `ZINC000179261199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179261199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000179261199 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 12, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 18, 11, 11, 6, 6, 16, 16, 16, 16, 16, 6, 3, 11, 11, 11, 11, 18, 18, 54, 11, 11, 11, 11, 6] 150 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000179261199 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179261199 Building ZINC000179286048 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179286048 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/232 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(C)C) `ZINC000179286048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179286048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000179286048 none CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 6, 2, 6, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 19, 4, 2, 3, 3, 19, 19, 19, 19, 19, 2, 2, 4, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/233 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(C)C) `ZINC000179286048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179286048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000179286048 none CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 6, 2, 6, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 19, 4, 2, 3, 3, 19, 19, 19, 19, 19, 2, 2, 4, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000179286048 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 Building ZINC000179286048 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179286048 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 232) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(C)C) `ZINC000179286048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179286048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000179286048 none CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 6, 2, 6, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 19, 4, 2, 3, 3, 19, 19, 19, 19, 19, 2, 2, 4, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 233) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(C)C) `ZINC000179286048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179286048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000179286048 none CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 6, 2, 6, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 19, 4, 2, 3, 3, 19, 19, 19, 19, 19, 2, 2, 4, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000179286048 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000179286048 Building ZINC000271818615 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000271818615 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/234 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000271818615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000271818615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000271818615 none CC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 9, 3, 9, 9, 27, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 27, 27, 81, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 243 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/235 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000271818615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000271818615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000271818615 none CC[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 9, 2, 9, 9, 30, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 30, 30, 90, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 288 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000271818615 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 Building ZINC000271818615 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000271818615 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 234) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000271818615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000271818615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000271818615 none CC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 9, 3, 9, 9, 27, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 27, 27, 81, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 243 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 235) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000271818615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000271818615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000271818615 none CC[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 9, 2, 9, 9, 30, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 30, 30, 90, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 288 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000271818615 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000271818615 Building ZINC000106499816 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106499816 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/236 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)CC2)cc1) `ZINC000106499816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106499816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000106499816 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)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', 'S.o', 'O.2', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 5, 10, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4] 23 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/237 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)CC2)cc1) `ZINC000106499816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106499816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000106499816 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)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', 'S.o', 'O.2', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 4, 8, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5] 23 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]) total number of confs: 33 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106499816 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 Building ZINC000106499816 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106499816 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 236) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)CC2)cc1) `ZINC000106499816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106499816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000106499816 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)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', 'S.o', 'O.2', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 5, 10, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4] 23 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 237) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)CC2)cc1) `ZINC000106499816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106499816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000106499816 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)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', 'S.o', 'O.2', 'C.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 4, 8, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5] 23 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]) total number of confs: 33 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106499816 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106499816 Building ZINC000115303251 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115303251 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/238 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000115303251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115303251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000115303251 none CC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 17 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]) total number of confs: 28 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/239 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000115303251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115303251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000115303251 none CC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4] 14 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]) total number of confs: 29 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000115303251 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 Building ZINC000115303251 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115303251 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 238) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000115303251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115303251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000115303251 none CC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 17 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]) total number of confs: 28 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 239) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000115303251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115303251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000115303251 none CC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4] 14 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]) total number of confs: 29 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000115303251 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303251 Building ZINC000115303252 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115303252 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/240 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000115303252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115303252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000115303252 none CC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 15 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]) total number of confs: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/241 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000115303252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115303252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000115303252 none CC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [11, 9, 9, 9, 9, 9, 9, 9, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6] 20 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]) total number of confs: 36 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000115303252 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 Building ZINC000115303252 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115303252 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 240) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000115303252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115303252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000115303252 none CC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 15 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]) total number of confs: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 241) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000115303252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115303252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000115303252 none CC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [11, 9, 9, 9, 9, 9, 9, 9, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6] 20 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]) total number of confs: 36 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000115303252 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000115303252 Building ZINC000106786796 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106786796 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/242 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 30, 37, 37, 37, 37, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/243 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 29, 35, 35, 35, 35, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/244 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/244' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 30, 37, 37, 37, 37, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/245 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/245' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 29, 35, 35, 35, 35, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106786796 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 Building ZINC000106786796 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106786796 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 242) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 30, 37, 37, 37, 37, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 243) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 29, 35, 35, 35, 35, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 244) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 30, 37, 37, 37, 37, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 245) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 29, 35, 35, 35, 35, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106786796 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 Building ZINC000106786796 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106786796 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 242) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 30, 37, 37, 37, 37, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 243) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 29, 35, 35, 35, 35, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 244) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 30, 37, 37, 37, 37, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 245) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 29, 35, 35, 35, 35, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106786796 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 Building ZINC000106786796 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106786796 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 242) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 30, 37, 37, 37, 37, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 243) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 29, 35, 35, 35, 35, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 244) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 30, 37, 37, 37, 37, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 245) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106786796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786796 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 24, 25, 25, 25, 29, 35, 35, 35, 35, 25, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106786796 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786796 Building ZINC000106786799 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106786799 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/246 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 25, 26, 26, 26, 31, 38, 38, 38, 38, 26, 8, 8, 8, 8, 8, 8, 4, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/247 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 25, 27, 27, 27, 31, 35, 35, 35, 35, 27, 8, 8, 8, 8, 8, 8, 3, 27, 27, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/248 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/248' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 25, 26, 26, 26, 31, 38, 38, 38, 38, 26, 8, 8, 8, 8, 8, 8, 4, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/249 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/249' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 25, 27, 27, 27, 31, 35, 35, 35, 35, 27, 8, 8, 8, 8, 8, 8, 3, 27, 27, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106786799 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 Building ZINC000106786799 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106786799 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 246) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 25, 26, 26, 26, 31, 38, 38, 38, 38, 26, 8, 8, 8, 8, 8, 8, 4, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 247) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 25, 27, 27, 27, 31, 35, 35, 35, 35, 27, 8, 8, 8, 8, 8, 8, 3, 27, 27, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 248) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 25, 26, 26, 26, 31, 38, 38, 38, 38, 26, 8, 8, 8, 8, 8, 8, 4, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 249) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 25, 27, 27, 27, 31, 35, 35, 35, 35, 27, 8, 8, 8, 8, 8, 8, 3, 27, 27, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106786799 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 Building ZINC000106786799 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106786799 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 246) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 25, 26, 26, 26, 31, 38, 38, 38, 38, 26, 8, 8, 8, 8, 8, 8, 4, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 247) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 25, 27, 27, 27, 31, 35, 35, 35, 35, 27, 8, 8, 8, 8, 8, 8, 3, 27, 27, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 248) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 25, 26, 26, 26, 31, 38, 38, 38, 38, 26, 8, 8, 8, 8, 8, 8, 4, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 249) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 25, 27, 27, 27, 31, 35, 35, 35, 35, 27, 8, 8, 8, 8, 8, 8, 3, 27, 27, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106786799 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 Building ZINC000106786799 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106786799 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 246) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 25, 26, 26, 26, 31, 38, 38, 38, 38, 26, 8, 8, 8, 8, 8, 8, 4, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 247) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 25, 27, 27, 27, 31, 35, 35, 35, 35, 27, 8, 8, 8, 8, 8, 8, 3, 27, 27, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 248) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 25, 26, 26, 26, 31, 38, 38, 38, 38, 26, 8, 8, 8, 8, 8, 8, 4, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 249) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1) `ZINC000106786799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106786799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000106786799 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 25, 27, 27, 27, 31, 35, 35, 35, 35, 27, 8, 8, 8, 8, 8, 8, 3, 27, 27, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106786799 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106786799 Building ZINC000274189352 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274189352 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/250 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCNC(C)=O)cc1Cl) `ZINC000274189352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274189352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000274189352 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCNC(C)=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', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 20, 20, 20, 4, 4, 4, 10, 10, 10, 4, 4, 2, 9, 9, 14, 14, 20, 20, 20, 20, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/251 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCNC(C)=O)cc1Cl) `ZINC000274189352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274189352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000274189352 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCNC(C)=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', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 20, 20, 20, 4, 4, 4, 10, 10, 10, 4, 4, 2, 9, 9, 14, 14, 20, 20, 20, 20, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000274189352 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 Building ZINC000274189352 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274189352 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 250) grep: /scratch/xiaobo/170854/xdl-8058088.90/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([C@]([O-])([SiH3])C(=O)NCCNC(C)=O)cc1Cl) `ZINC000274189352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274189352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000274189352 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCNC(C)=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', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 20, 20, 20, 4, 4, 4, 10, 10, 10, 4, 4, 2, 9, 9, 14, 14, 20, 20, 20, 20, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 251) grep: /scratch/xiaobo/170854/xdl-8058088.90/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([C@@]([O-])([SiH3])C(=O)NCCNC(C)=O)cc1Cl) `ZINC000274189352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274189352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000274189352 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCNC(C)=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', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 14, 20, 20, 20, 4, 4, 4, 10, 10, 10, 4, 4, 2, 9, 9, 14, 14, 20, 20, 20, 20, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000274189352 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000274189352 Building ZINC001026222150 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001026222150 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/252 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@@H](NCCO)[C@H]2C1) `ZINC001026222150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001026222150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001026222150 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@@H](NCCO)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 23, 48, 50, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 23, 48, 48, 50, 50, 150, 12, 12] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 347 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/253 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@@H](NCCO)[C@H]2C1) `ZINC001026222150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001026222150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001026222150 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@@H](NCCO)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 25, 48, 50, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 25, 48, 48, 50, 50, 150, 11, 11] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 347 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001026222150 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 Building ZINC001026222150 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001026222150 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 252) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@@H](NCCO)[C@H]2C1) `ZINC001026222150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001026222150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001026222150 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@@H](NCCO)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 23, 48, 50, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 23, 48, 48, 50, 50, 150, 12, 12] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 347 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 253) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@@H](NCCO)[C@H]2C1) `ZINC001026222150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001026222150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001026222150 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@@H](NCCO)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 25, 48, 50, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 25, 48, 48, 50, 50, 150, 11, 11] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 347 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001026222150 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222150 Building ZINC001026222152 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001026222152 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/254 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](NCCO)[C@@H]2C1) `ZINC001026222152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001026222152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001026222152 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](NCCO)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 29, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 29, 50, 50, 50, 50, 150, 12, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 331 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/255 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](NCCO)[C@@H]2C1) `ZINC001026222152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001026222152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001026222152 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](NCCO)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 10, 10, 10, 10, 10, 10, 10, 10, 32, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 32, 50, 50, 50, 50, 150, 10, 10] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 334 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001026222152 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 Building ZINC001026222152 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001026222152 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 254) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](NCCO)[C@@H]2C1) `ZINC001026222152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001026222152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001026222152 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](NCCO)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 29, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 29, 50, 50, 50, 50, 150, 12, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 331 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 255) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](NCCO)[C@@H]2C1) `ZINC001026222152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001026222152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001026222152 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](NCCO)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 10, 10, 10, 10, 10, 10, 10, 10, 32, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 32, 50, 50, 50, 50, 150, 10, 10] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 334 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001026222152 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026222152 Building ZINC000378224431 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378224431 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/256 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H]3CCCN3)CC2)cn1) `ZINC000378224431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378224431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000378224431 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H]3CCCN3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 7, 13, 13, 13, 18, 31, 31, 31, 31, 31, 13, 13, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 13, 13, 13, 13, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 80 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/257 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@H]3CCCN3)CC2)cn1) `ZINC000378224431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378224431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000378224431 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@H]3CCCN3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 7, 12, 12, 12, 18, 31, 31, 31, 31, 31, 12, 12, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 31, 12, 12, 12, 12, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378224431 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 Building ZINC000378224431 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378224431 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 256) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H]3CCCN3)CC2)cn1) `ZINC000378224431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378224431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000378224431 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H]3CCCN3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 7, 13, 13, 13, 18, 31, 31, 31, 31, 31, 13, 13, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 13, 13, 13, 13, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 80 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 257) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@H]3CCCN3)CC2)cn1) `ZINC000378224431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378224431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000378224431 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@H]3CCCN3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 7, 12, 12, 12, 18, 31, 31, 31, 31, 31, 12, 12, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 31, 12, 12, 12, 12, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378224431 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224431 Building ZINC000378224432 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378224432 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/258 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H]3CCCN3)CC2)cn1) `ZINC000378224432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378224432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000378224432 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H]3CCCN3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 7, 13, 13, 13, 19, 32, 32, 32, 32, 32, 13, 13, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/259 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H]3CCCN3)CC2)cn1) `ZINC000378224432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378224432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000378224432 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H]3CCCN3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 7, 11, 11, 11, 22, 29, 29, 29, 29, 29, 11, 11, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 11, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378224432 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 Building ZINC000378224432 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378224432 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 258) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H]3CCCN3)CC2)cn1) `ZINC000378224432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378224432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000378224432 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H]3CCCN3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 7, 13, 13, 13, 19, 32, 32, 32, 32, 32, 13, 13, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 259) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H]3CCCN3)CC2)cn1) `ZINC000378224432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378224432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000378224432 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H]3CCCN3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 7, 11, 11, 11, 22, 29, 29, 29, 29, 29, 11, 11, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 11, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378224432 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378224432 Building ZINC000107185502 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107185502 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/260 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O) `ZINC000107185502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107185502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000107185502 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [29, 13, 29, 4, 13, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 25, 25, 29, 29, 29, 29, 29, 29, 29, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 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]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/261 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O) `ZINC000107185502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107185502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000107185502 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [25, 11, 25, 4, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 11, 21, 21, 25, 25, 25, 25, 25, 25, 25, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21] 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]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000107185502 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 Building ZINC000107185502 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107185502 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 260) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O) `ZINC000107185502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107185502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000107185502 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [29, 13, 29, 4, 13, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 25, 25, 29, 29, 29, 29, 29, 29, 29, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 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]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 261) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O) `ZINC000107185502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107185502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000107185502 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [25, 11, 25, 4, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 11, 21, 21, 25, 25, 25, 25, 25, 25, 25, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21] 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]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000107185502 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107185502 Building ZINC000647680075 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647680075 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/262 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1SCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647680075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680075 none C[C@H]1SCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [23, 23, 23, 23, 23, 23, 10, 23, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 6, 12, 12, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/263 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1SCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647680075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680075 none C[C@H]1SCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [20, 20, 20, 20, 20, 20, 8, 20, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 4, 12, 12, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647680075 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 Building ZINC000647680075 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647680075 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 262) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1SCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647680075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680075 none C[C@H]1SCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [23, 23, 23, 23, 23, 23, 10, 23, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 6, 12, 12, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 263) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1SCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647680075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680075 none C[C@H]1SCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [20, 20, 20, 20, 20, 20, 8, 20, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 4, 12, 12, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647680075 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680075 Building ZINC000647680076 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647680076 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/264 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1SCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647680076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680076 none C[C@@H]1SCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [23, 23, 23, 23, 23, 23, 11, 23, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 6, 12, 12, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/265 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1SCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647680076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680076 none C[C@@H]1SCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [19, 19, 19, 19, 19, 19, 9, 19, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 5, 12, 12, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647680076 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 Building ZINC000647680076 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647680076 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 264) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1SCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647680076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680076 none C[C@@H]1SCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [23, 23, 23, 23, 23, 23, 11, 23, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 6, 12, 12, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 265) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1SCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647680076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680076 none C[C@@H]1SCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [19, 19, 19, 19, 19, 19, 9, 19, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 5, 12, 12, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647680076 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680076 Building ZINC000647680077 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647680077 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/266 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1SCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647680077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680077 none C[C@@H]1SCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [20, 20, 20, 20, 20, 20, 8, 20, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 4, 12, 12, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/267 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1SCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647680077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680077 none C[C@@H]1SCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [24, 24, 24, 24, 24, 24, 10, 24, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 6, 12, 12, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647680077 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 Building ZINC000647680077 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647680077 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 266) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1SCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647680077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680077 none C[C@@H]1SCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [20, 20, 20, 20, 20, 20, 8, 20, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 4, 12, 12, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 267) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1SCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647680077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680077 none C[C@@H]1SCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [24, 24, 24, 24, 24, 24, 10, 24, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 6, 12, 12, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647680077 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680077 Building ZINC000647680078 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647680078 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/268 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1SCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647680078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680078 none C[C@H]1SCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [18, 18, 18, 18, 18, 18, 9, 18, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 5, 12, 12, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/269 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1SCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647680078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680078 none C[C@H]1SCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [23, 23, 23, 23, 23, 23, 11, 23, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 6, 12, 12, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647680078 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 Building ZINC000647680078 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647680078 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 268) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1SCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647680078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680078 none C[C@H]1SCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [18, 18, 18, 18, 18, 18, 9, 18, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 5, 12, 12, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 269) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1SCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000647680078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647680078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000647680078 none C[C@H]1SCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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: [23, 23, 23, 23, 23, 23, 11, 23, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 6, 12, 12, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000647680078 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000647680078 Building ZINC000378265034 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378265034 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/270 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H](C)C1) `ZINC000378265034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378265034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000378265034 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 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, 5, 5, 1, 1, 1, 2, 15, 30, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 48 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/271 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H](C)C1) `ZINC000378265034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378265034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000378265034 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 18, 30, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378265034 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 Building ZINC000378265034 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378265034 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 270) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H](C)C1) `ZINC000378265034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378265034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000378265034 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 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, 5, 5, 1, 1, 1, 2, 15, 30, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 48 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 271) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H](C)C1) `ZINC000378265034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378265034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000378265034 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 18, 30, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378265034 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265034 Building ZINC000378265035 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378265035 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/272 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H](C)C1) `ZINC000378265035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378265035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000378265035 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 31, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 71 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/273 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H](C)C1) `ZINC000378265035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378265035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000378265035 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 29, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378265035 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 Building ZINC000378265035 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378265035 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 272) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H](C)C1) `ZINC000378265035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378265035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000378265035 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 31, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 71 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 273) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H](C)C1) `ZINC000378265035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378265035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000378265035 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 29, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378265035 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378265035 Building ZINC000107599635 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107599635 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/274 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCCC3)C2)cn1) `ZINC000107599635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107599635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000107599635 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 8, 12, 20, 20, 20, 20, 20, 22, 31, 31, 31, 28, 20, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 75 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/275 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCCC3)C2)cn1) `ZINC000107599635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107599635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000107599635 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 7, 13, 20, 20, 20, 20, 20, 21, 32, 32, 32, 30, 20, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 70 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000107599635 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 Building ZINC000107599635 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107599635 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 274) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCCC3)C2)cn1) `ZINC000107599635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107599635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000107599635 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 8, 12, 20, 20, 20, 20, 20, 22, 31, 31, 31, 28, 20, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 75 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 275) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCCC3)C2)cn1) `ZINC000107599635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107599635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000107599635 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 7, 13, 20, 20, 20, 20, 20, 21, 32, 32, 32, 30, 20, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 70 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000107599635 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599635 Building ZINC000107599639 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107599639 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/276 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCCC3)C2)cn1) `ZINC000107599639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107599639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000107599639 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 8, 10, 17, 17, 17, 17, 17, 20, 31, 31, 31, 28, 17, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/277 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCCC3)C2)cn1) `ZINC000107599639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107599639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000107599639 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 8, 9, 17, 17, 17, 17, 17, 20, 32, 32, 32, 30, 17, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 74 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000107599639 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 Building ZINC000107599639 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107599639 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 276) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCCC3)C2)cn1) `ZINC000107599639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107599639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000107599639 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 8, 10, 17, 17, 17, 17, 17, 20, 31, 31, 31, 28, 17, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 277) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCCC3)C2)cn1) `ZINC000107599639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107599639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000107599639 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 8, 9, 17, 17, 17, 17, 17, 20, 32, 32, 32, 30, 17, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 74 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000107599639 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000107599639 Building ZINC000836867377 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000836867377 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/278 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C[C@H]2CC[C@@H](C1)O2) `ZINC000836867377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000836867377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000836867377 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C[C@H]2CC[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 19, 19, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/279 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C[C@H]2CC[C@@H](C1)O2) `ZINC000836867377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000836867377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000836867377 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C[C@H]2CC[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000836867377 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 Building ZINC000836867377 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000836867377 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 278) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C[C@H]2CC[C@@H](C1)O2) `ZINC000836867377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000836867377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000836867377 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C[C@H]2CC[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 19, 19, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 279) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C[C@H]2CC[C@@H](C1)O2) `ZINC000836867377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000836867377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000836867377 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C[C@H]2CC[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000836867377 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000836867377 Building ZINC000339136321 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339136321 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/280 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339136321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339136321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000339136321 none CN[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 21, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 24, 24, 24, 24, 21, 21, 21, 15, 15, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/281 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339136321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339136321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000339136321 none CN[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 22, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 24, 24, 24, 24, 23, 23, 23, 13, 13, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000339136321 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 Building ZINC000339136321 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339136321 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 280) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339136321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339136321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000339136321 none CN[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 21, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 24, 24, 24, 24, 21, 21, 21, 15, 15, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 281) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339136321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339136321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000339136321 none CN[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 22, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 24, 24, 24, 24, 23, 23, 23, 13, 13, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000339136321 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136321 Building ZINC000339136322 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339136322 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/282 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339136322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339136322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000339136322 none CN[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 13, 24, 23, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 26, 26, 26, 26, 24, 24, 24, 13, 13, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/283 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339136322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339136322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000339136322 none CN[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 19, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 23, 23, 23, 23, 20, 20, 20, 13, 13, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000339136322 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 Building ZINC000339136322 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339136322 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 282) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339136322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339136322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000339136322 none CN[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 13, 24, 23, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 26, 26, 26, 26, 24, 24, 24, 13, 13, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 283) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339136322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339136322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000339136322 none CN[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 19, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 23, 23, 23, 23, 20, 20, 20, 13, 13, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000339136322 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339136322 Building ZINC000416291320 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416291320 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/284 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000416291320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416291320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000416291320 none COC(=O)C(C)(C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 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: [47, 47, 22, 47, 5, 22, 22, 4, 5, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 47, 47, 47, 22, 22, 22, 22, 22, 22, 5, 5, 5, 4, 4, 8, 4, 4] 100 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/285 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000416291320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416291320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000416291320 none COC(=O)C(C)(C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 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: [47, 47, 21, 47, 5, 21, 21, 4, 5, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 47, 47, 47, 21, 21, 21, 21, 21, 21, 5, 5, 5, 4, 4, 8, 4, 4] 100 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416291320 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 Building ZINC000416291320 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416291320 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 284) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000416291320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416291320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000416291320 none COC(=O)C(C)(C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 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: [47, 47, 22, 47, 5, 22, 22, 4, 5, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 47, 47, 47, 22, 22, 22, 22, 22, 22, 5, 5, 5, 4, 4, 8, 4, 4] 100 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 285) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000416291320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416291320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000416291320 none COC(=O)C(C)(C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 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: [47, 47, 21, 47, 5, 21, 21, 4, 5, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 47, 47, 47, 21, 21, 21, 21, 21, 21, 5, 5, 5, 4, 4, 8, 4, 4] 100 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416291320 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416291320 Building ZINC000644752174 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644752174 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/286 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F) `ZINC000644752174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644752174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752174 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 14, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 4, 10, 10, 10, 10, 10, 84] 150 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]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/287 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F) `ZINC000644752174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644752174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752174 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 5, 11, 11, 11, 11, 11, 84] 150 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]) total number of confs: 202 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644752174 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 Building ZINC000644752174 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644752174 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 286) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F) `ZINC000644752174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644752174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752174 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 14, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 4, 10, 10, 10, 10, 10, 84] 150 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]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 287) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F) `ZINC000644752174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644752174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752174 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 5, 11, 11, 11, 11, 11, 84] 150 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]) total number of confs: 202 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644752174 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752174 Building ZINC000644752178 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644752178 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/288 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F) `ZINC000644752178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644752178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752178 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 13, 29, 29, 29, 29, 29, 29, 13, 13, 13, 5, 11, 11, 11, 11, 11, 87] 150 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]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/289 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F) `ZINC000644752178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644752178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752178 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 16, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 16, 23, 23, 23, 23, 23, 23, 16, 16, 16, 5, 11, 11, 11, 11, 11, 69] 150 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644752178 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 Building ZINC000644752178 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644752178 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 288) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F) `ZINC000644752178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644752178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752178 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 13, 29, 29, 29, 29, 29, 29, 13, 13, 13, 5, 11, 11, 11, 11, 11, 87] 150 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]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 289) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F) `ZINC000644752178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644752178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752178 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 16, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 16, 23, 23, 23, 23, 23, 23, 16, 16, 16, 5, 11, 11, 11, 11, 11, 69] 150 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644752178 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752178 Building ZINC000644752180 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644752180 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/290 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F) `ZINC000644752180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644752180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752180 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 19, 30, 30, 30, 30, 30, 30, 19, 19, 19, 6, 10, 10, 10, 10, 10, 90] 150 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]) total number of confs: 218 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/291 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F) `ZINC000644752180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644752180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752180 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 15, 29, 29, 28, 29, 29, 29, 15, 15, 15, 5, 12, 12, 12, 12, 12, 87] 150 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]) total number of confs: 220 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644752180 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 Building ZINC000644752180 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644752180 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 290) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F) `ZINC000644752180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644752180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752180 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 19, 30, 30, 30, 30, 30, 30, 19, 19, 19, 6, 10, 10, 10, 10, 10, 90] 150 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]) total number of confs: 218 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 291) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F) `ZINC000644752180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644752180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752180 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 15, 29, 29, 28, 29, 29, 29, 15, 15, 15, 5, 12, 12, 12, 12, 12, 87] 150 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]) total number of confs: 220 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644752180 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752180 Building ZINC000644752184 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644752184 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/292 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F) `ZINC000644752184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644752184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752184 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 17, 29, 29, 29, 29, 29, 29, 17, 17, 17, 5, 12, 12, 12, 12, 12, 87] 150 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]) total number of confs: 221 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/293 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F) `ZINC000644752184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644752184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752184 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 20, 31, 31, 31, 31, 31, 31, 20, 20, 20, 6, 12, 12, 12, 12, 12, 93] 150 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]) total number of confs: 229 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644752184 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 Building ZINC000644752184 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644752184 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 292) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F) `ZINC000644752184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644752184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752184 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 17, 29, 29, 29, 29, 29, 29, 17, 17, 17, 5, 12, 12, 12, 12, 12, 87] 150 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]) total number of confs: 221 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 293) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F) `ZINC000644752184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644752184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000644752184 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 20, 31, 31, 31, 31, 31, 31, 20, 20, 20, 6, 12, 12, 12, 12, 12, 93] 150 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]) total number of confs: 229 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644752184 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644752184 Building ZINC000416308982 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416308982 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/294 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC000416308982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416308982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416308982 none CN(C)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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: [42, 41, 42, 24, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 41, 41, 42, 42, 42, 42, 42, 42, 24, 24, 6, 5, 5, 10, 5, 5, 41, 41, 41, 41] 100 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 168 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/295 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC000416308982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416308982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416308982 none CN(C)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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: [42, 42, 42, 25, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 25, 25, 6, 5, 5, 10, 5, 5, 42, 42, 42, 42] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416308982 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 Building ZINC000416308982 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416308982 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 294) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(C)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC000416308982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416308982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416308982 none CN(C)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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: [42, 41, 42, 24, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 41, 41, 42, 42, 42, 42, 42, 42, 24, 24, 6, 5, 5, 10, 5, 5, 41, 41, 41, 41] 100 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 168 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 295) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(C)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC000416308982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416308982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416308982 none CN(C)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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: [42, 42, 42, 25, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 25, 25, 6, 5, 5, 10, 5, 5, 42, 42, 42, 42] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416308982 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416308982 Building ZINC000416346374 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416346374 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/296 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 21, 23, 23, 23, 23, 42, 47, 47, 23, 4, 4, 4, 4, 4, 4, 3, 23, 23, 23, 23, 42, 42, 47, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/297 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 25, 25, 25, 25, 44, 49, 49, 25, 4, 4, 4, 4, 4, 4, 3, 25, 25, 25, 25, 44, 44, 49, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/298 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/298' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 21, 23, 23, 23, 23, 42, 47, 47, 23, 4, 4, 4, 4, 4, 4, 3, 23, 23, 23, 23, 42, 42, 47, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/299 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/299' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 25, 25, 25, 25, 44, 49, 49, 25, 4, 4, 4, 4, 4, 4, 3, 25, 25, 25, 25, 44, 44, 49, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416346374 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 Building ZINC000416346374 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416346374 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 296) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 21, 23, 23, 23, 23, 42, 47, 47, 23, 4, 4, 4, 4, 4, 4, 3, 23, 23, 23, 23, 42, 42, 47, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 297) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 25, 25, 25, 25, 44, 49, 49, 25, 4, 4, 4, 4, 4, 4, 3, 25, 25, 25, 25, 44, 44, 49, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 298) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 21, 23, 23, 23, 23, 42, 47, 47, 23, 4, 4, 4, 4, 4, 4, 3, 23, 23, 23, 23, 42, 42, 47, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 299) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 25, 25, 25, 25, 44, 49, 49, 25, 4, 4, 4, 4, 4, 4, 3, 25, 25, 25, 25, 44, 44, 49, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416346374 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 Building ZINC000416346374 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416346374 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 296) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 21, 23, 23, 23, 23, 42, 47, 47, 23, 4, 4, 4, 4, 4, 4, 3, 23, 23, 23, 23, 42, 42, 47, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 297) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 25, 25, 25, 25, 44, 49, 49, 25, 4, 4, 4, 4, 4, 4, 3, 25, 25, 25, 25, 44, 44, 49, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 298) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 21, 23, 23, 23, 23, 42, 47, 47, 23, 4, 4, 4, 4, 4, 4, 3, 23, 23, 23, 23, 42, 42, 47, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 299) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 25, 25, 25, 25, 44, 49, 49, 25, 4, 4, 4, 4, 4, 4, 3, 25, 25, 25, 25, 44, 44, 49, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416346374 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 Building ZINC000416346374 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416346374 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 296) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 21, 23, 23, 23, 23, 42, 47, 47, 23, 4, 4, 4, 4, 4, 4, 3, 23, 23, 23, 23, 42, 42, 47, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 297) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 25, 25, 25, 25, 44, 49, 49, 25, 4, 4, 4, 4, 4, 4, 3, 25, 25, 25, 25, 44, 44, 49, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 298) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 21, 23, 23, 23, 23, 42, 47, 47, 23, 4, 4, 4, 4, 4, 4, 3, 23, 23, 23, 23, 42, 42, 47, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 299) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1) `ZINC000416346374.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416346374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346374 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 25, 25, 25, 25, 44, 49, 49, 25, 4, 4, 4, 4, 4, 4, 3, 25, 25, 25, 25, 44, 44, 49, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416346374 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346374 Building ZINC000416346375 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416346375 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/300 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 24, 24, 24, 24, 44, 49, 49, 24, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 44, 44, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/301 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 22, 24, 24, 24, 24, 43, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 43, 43, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/302 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/302' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 24, 24, 24, 24, 44, 49, 49, 24, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 44, 44, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/303 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/303' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 22, 24, 24, 24, 24, 43, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 43, 43, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416346375 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 Building ZINC000416346375 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416346375 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 300) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 24, 24, 24, 24, 44, 49, 49, 24, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 44, 44, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 301) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 22, 24, 24, 24, 24, 43, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 43, 43, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 302) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 24, 24, 24, 24, 44, 49, 49, 24, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 44, 44, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 303) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 22, 24, 24, 24, 24, 43, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 43, 43, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416346375 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 Building ZINC000416346375 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416346375 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 300) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 24, 24, 24, 24, 44, 49, 49, 24, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 44, 44, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 301) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 22, 24, 24, 24, 24, 43, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 43, 43, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 302) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 24, 24, 24, 24, 44, 49, 49, 24, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 44, 44, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 303) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 22, 24, 24, 24, 24, 43, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 43, 43, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416346375 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 Building ZINC000416346375 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416346375 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 300) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 24, 24, 24, 24, 44, 49, 49, 24, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 44, 44, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 301) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 22, 24, 24, 24, 24, 43, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 43, 43, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 302) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 22, 24, 24, 24, 24, 44, 49, 49, 24, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 44, 44, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 303) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1) `ZINC000416346375.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416346375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000416346375 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 22, 24, 24, 24, 24, 43, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 43, 43, 49, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000416346375 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000416346375 Building ZINC000026098320 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000026098320 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/304 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCC(=O)NC(C)C)cc1) `ZINC000026098320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000026098320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000026098320 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCC(=O)NC(C)C)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 20, 37, 37, 37, 43, 43, 3, 3, 3, 3, 3, 3, 3, 5, 20, 20, 37, 43, 43, 43, 43, 43, 43, 43, 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]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/305 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCC(=O)NC(C)C)cc1) `ZINC000026098320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000026098320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000026098320 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCC(=O)NC(C)C)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 20, 38, 38, 38, 43, 43, 3, 3, 3, 3, 3, 3, 3, 5, 20, 20, 38, 43, 43, 43, 43, 43, 43, 43, 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]) total number of confs: 174 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000026098320 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 Building ZINC000026098320 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000026098320 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 304) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCC(=O)NC(C)C)cc1) `ZINC000026098320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000026098320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000026098320 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCC(=O)NC(C)C)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 20, 37, 37, 37, 43, 43, 3, 3, 3, 3, 3, 3, 3, 5, 20, 20, 37, 43, 43, 43, 43, 43, 43, 43, 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]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 305) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NCC(=O)NC(C)C)cc1) `ZINC000026098320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000026098320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000026098320 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCC(=O)NC(C)C)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 20, 38, 38, 38, 43, 43, 3, 3, 3, 3, 3, 3, 3, 5, 20, 20, 38, 43, 43, 43, 43, 43, 43, 43, 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]) total number of confs: 174 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000026098320 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000026098320 Building ZINC000644754891 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644754891 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/306 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](O)C(F)(F)F)cn1) `ZINC000644754891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644754891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000644754891 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](O)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 14, 14, 14, 14, 14, 14, 7, 7, 19, 19, 19, 19, 19, 7, 4, 9, 9, 9, 42, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/307 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](O)C(F)(F)F)cn1) `ZINC000644754891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644754891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000644754891 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](O)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 16, 16, 16, 16, 16, 16, 7, 7, 20, 20, 20, 20, 20, 7, 4, 11, 11, 11, 48, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644754891 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 Building ZINC000644754891 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644754891 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 306) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](O)C(F)(F)F)cn1) `ZINC000644754891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644754891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000644754891 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](O)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 14, 14, 14, 14, 14, 14, 7, 7, 19, 19, 19, 19, 19, 7, 4, 9, 9, 9, 42, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 307) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](O)C(F)(F)F)cn1) `ZINC000644754891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644754891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000644754891 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](O)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 16, 16, 16, 16, 16, 16, 7, 7, 20, 20, 20, 20, 20, 7, 4, 11, 11, 11, 48, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644754891 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754891 Building ZINC000644754899 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644754899 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/308 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](O)C(F)(F)F)cn1) `ZINC000644754899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644754899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000644754899 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](O)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 14, 14, 14, 14, 14, 14, 7, 7, 21, 21, 21, 21, 21, 7, 4, 10, 10, 10, 42, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/309 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](O)C(F)(F)F)cn1) `ZINC000644754899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644754899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000644754899 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](O)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 13, 13, 13, 13, 13, 13, 7, 7, 22, 22, 22, 22, 22, 7, 4, 11, 11, 11, 39, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644754899 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 Building ZINC000644754899 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644754899 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 308) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](O)C(F)(F)F)cn1) `ZINC000644754899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644754899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000644754899 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](O)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 14, 14, 14, 14, 14, 14, 7, 7, 21, 21, 21, 21, 21, 7, 4, 10, 10, 10, 42, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 309) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](O)C(F)(F)F)cn1) `ZINC000644754899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644754899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000644754899 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](O)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 13, 13, 13, 13, 13, 13, 7, 7, 22, 22, 22, 22, 22, 7, 4, 11, 11, 11, 39, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644754899 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644754899 Building ZINC000644758804 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644758804 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/310 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H](O)C(F)(F)F) `ZINC000644758804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644758804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758804 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 16, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 16, 34, 34, 34, 34, 34, 34, 16, 16, 16, 4, 6, 6, 6, 6, 6, 6, 102] 150 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]) total number of confs: 243 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/311 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H](O)C(F)(F)F) `ZINC000644758804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644758804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758804 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 5, 19, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 19, 41, 41, 41, 41, 41, 41, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 123] 150 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]) total number of confs: 295 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644758804 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 Building ZINC000644758804 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644758804 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 310) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H](O)C(F)(F)F) `ZINC000644758804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644758804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758804 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 16, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 16, 34, 34, 34, 34, 34, 34, 16, 16, 16, 4, 6, 6, 6, 6, 6, 6, 102] 150 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]) total number of confs: 243 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 311) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H](O)C(F)(F)F) `ZINC000644758804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644758804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758804 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 5, 19, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 19, 41, 41, 41, 41, 41, 41, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 123] 150 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]) total number of confs: 295 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644758804 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758804 Building ZINC000644758807 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644758807 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/312 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F) `ZINC000644758807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644758807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758807 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 7, 25, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 8, 25, 39, 39, 39, 39, 39, 39, 25, 25, 25, 7, 8, 8, 8, 8, 8, 8, 117] 150 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]) total number of confs: 281 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/313 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F) `ZINC000644758807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644758807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758807 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 18, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 18, 38, 38, 38, 38, 38, 38, 18, 18, 18, 5, 6, 6, 6, 6, 6, 6, 114] 150 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]) total number of confs: 278 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644758807 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 Building ZINC000644758807 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644758807 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 312) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F) `ZINC000644758807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644758807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758807 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 7, 25, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 8, 25, 39, 39, 39, 39, 39, 39, 25, 25, 25, 7, 8, 8, 8, 8, 8, 8, 117] 150 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]) total number of confs: 281 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 313) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F) `ZINC000644758807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644758807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758807 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 18, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 18, 38, 38, 38, 38, 38, 38, 18, 18, 18, 5, 6, 6, 6, 6, 6, 6, 114] 150 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]) total number of confs: 278 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644758807 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758807 Building ZINC000644758810 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644758810 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/314 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F) `ZINC000644758810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644758810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758810 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 18, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 18, 42, 42, 42, 42, 42, 42, 18, 18, 18, 5, 6, 6, 6, 6, 6, 6, 126] 150 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]) total number of confs: 305 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/315 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F) `ZINC000644758810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644758810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758810 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 24, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 8, 24, 36, 36, 36, 36, 36, 36, 24, 24, 24, 7, 8, 8, 8, 8, 8, 8, 108] 150 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]) total number of confs: 257 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644758810 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 Building ZINC000644758810 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644758810 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 314) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F) `ZINC000644758810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644758810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758810 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 18, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 18, 42, 42, 42, 42, 42, 42, 18, 18, 18, 5, 6, 6, 6, 6, 6, 6, 126] 150 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]) total number of confs: 305 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 315) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F) `ZINC000644758810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644758810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000644758810 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 24, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 8, 24, 36, 36, 36, 36, 36, 36, 24, 24, 24, 7, 8, 8, 8, 8, 8, 8, 108] 150 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]) total number of confs: 257 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000644758810 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000644758810 Building ZINC000408069283 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069283 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/316 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/317 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/318 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/318' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 9, 2, 9, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14] 42 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 40 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/319 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/319' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 9, 2, 9, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14] 42 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 40 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069283 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 Building ZINC000408069283 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069283 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 316) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 317) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 318) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 9, 2, 9, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14] 42 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 40 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 319) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 9, 2, 9, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14] 42 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 40 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069283 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 Building ZINC000408069283 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069283 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 316) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 317) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 318) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 9, 2, 9, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14] 42 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 40 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 319) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 9, 2, 9, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14] 42 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 40 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069283 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 Building ZINC000408069283 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069283 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 316) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 317) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 318) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 9, 2, 9, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14] 42 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 40 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 319) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C) `ZINC000408069283.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069283 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 9, 2, 9, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14] 42 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 40 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069283 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069283 Building ZINC000408069284 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069284 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/320 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 13, 1, 13, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/321 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 13, 1, 13, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/322 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/322' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 1, 14, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/323 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/323' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 1, 14, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069284 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 Building ZINC000408069284 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069284 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 320) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 13, 1, 13, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 321) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 13, 1, 13, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 322) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 1, 14, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 323) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 1, 14, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069284 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 Building ZINC000408069284 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069284 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 320) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 13, 1, 13, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 321) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 13, 1, 13, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 322) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 1, 14, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 323) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 1, 14, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069284 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 Building ZINC000408069284 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069284 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 320) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 13, 1, 13, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 321) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 13, 1, 13, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 322) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 1, 14, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 323) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069284.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069284 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 1, 14, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069284 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069284 Building ZINC000408069285 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069285 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/324 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 25, 27, 27, 27, 27, 27, 27, 27, 27, 19, 3, 19, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/325 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 25, 27, 27, 27, 27, 27, 27, 27, 27, 19, 3, 19, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/326 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/326' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 3, 16, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/327 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/327' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 3, 16, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069285 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 Building ZINC000408069285 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069285 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 324) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 25, 27, 27, 27, 27, 27, 27, 27, 27, 19, 3, 19, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 325) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 25, 27, 27, 27, 27, 27, 27, 27, 27, 19, 3, 19, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 326) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 3, 16, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 327) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 3, 16, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069285 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 Building ZINC000408069285 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069285 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 324) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 25, 27, 27, 27, 27, 27, 27, 27, 27, 19, 3, 19, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 325) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 25, 27, 27, 27, 27, 27, 27, 27, 27, 19, 3, 19, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 326) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 3, 16, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 327) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 3, 16, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069285 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 Building ZINC000408069285 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069285 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 324) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 25, 27, 27, 27, 27, 27, 27, 27, 27, 19, 3, 19, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 325) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 25, 27, 27, 27, 27, 27, 27, 27, 27, 19, 3, 19, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 326) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 3, 16, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 327) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408069285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069285 none C[C@@H]1CN(C)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 3, 16, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069285 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069285 Building ZINC000408069286 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069286 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/328 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/329 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/330 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/330' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 3, 17, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/331 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/331' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 3, 17, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069286 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 Building ZINC000408069286 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069286 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 328) grep: /scratch/xiaobo/170854/xdl-8058088.90/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]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 329) grep: /scratch/xiaobo/170854/xdl-8058088.90/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]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 330) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 3, 17, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 331) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 3, 17, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069286 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 Building ZINC000408069286 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069286 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 328) grep: /scratch/xiaobo/170854/xdl-8058088.90/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]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 329) grep: /scratch/xiaobo/170854/xdl-8058088.90/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]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 330) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 3, 17, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 331) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 3, 17, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069286 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 Building ZINC000408069286 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408069286 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 328) grep: /scratch/xiaobo/170854/xdl-8058088.90/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]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 329) grep: /scratch/xiaobo/170854/xdl-8058088.90/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]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 330) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 3, 17, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 331) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C) `ZINC000408069286.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408069286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408069286 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 3, 17, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408069286 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408069286 Building ZINC000182750100 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182750100 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/332 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/332' -> `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](C)C[S@](C)=O) `ZINC000182750100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182750100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000182750100 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[S@](C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 40, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 18, 40, 40, 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]) total number of confs: 194 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/333 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/333' -> `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](C)C[S@](C)=O) `ZINC000182750100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182750100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000182750100 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[S@](C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 38, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 16, 16, 16, 38, 38, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000182750100 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 Building ZINC000182750100 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182750100 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 332) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[S@](C)=O) `ZINC000182750100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182750100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000182750100 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[S@](C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 40, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 18, 40, 40, 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]) total number of confs: 194 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 333) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[S@](C)=O) `ZINC000182750100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182750100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000182750100 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[S@](C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 38, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 16, 16, 16, 38, 38, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000182750100 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182750100 Building ZINC000408074293 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074293 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/334 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 22 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/335 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 27 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/336 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/336' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 22 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/337 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/337' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 27 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074293 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 Building ZINC000408074293 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074293 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 334) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 22 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 335) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 27 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 336) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 22 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 337) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 27 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074293 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 Building ZINC000408074293 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074293 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 334) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 22 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 335) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 27 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 336) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 22 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 337) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 27 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074293 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 Building ZINC000408074293 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074293 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 334) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 22 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 335) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 27 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 336) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 22 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 337) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C) `ZINC000408074293.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074293 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 27 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074293 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074293 Building ZINC000408074295 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074295 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/338 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/339 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 42 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/340 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/340' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/341 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/341' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 42 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074295 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 Building ZINC000408074295 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074295 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 338) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 339) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 42 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 340) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 341) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 42 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074295 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 Building ZINC000408074295 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074295 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 338) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 339) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 42 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 340) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 341) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 42 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074295 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 Building ZINC000408074295 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074295 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 338) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 339) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 42 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 340) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 341) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C) `ZINC000408074295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074295 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 42 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074295 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074295 Building ZINC000408074296 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074296 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/342 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 16, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/343 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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, 3, 19, 22, 32, 32, 32, 32, 32, 32, 32, 31, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/344 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/344' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 16, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/345 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/345' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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, 3, 19, 22, 32, 32, 32, 32, 32, 32, 32, 31, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074296 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 Building ZINC000408074296 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074296 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 342) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 16, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 343) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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, 3, 19, 22, 32, 32, 32, 32, 32, 32, 32, 31, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 344) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 16, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 345) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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, 3, 19, 22, 32, 32, 32, 32, 32, 32, 32, 31, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074296 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 Building ZINC000408074296 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074296 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 342) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 16, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 343) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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, 3, 19, 22, 32, 32, 32, 32, 32, 32, 32, 31, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 344) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 16, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 345) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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, 3, 19, 22, 32, 32, 32, 32, 32, 32, 32, 31, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074296 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 Building ZINC000408074296 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074296 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 342) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 16, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 343) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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, 3, 19, 22, 32, 32, 32, 32, 32, 32, 32, 31, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 344) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 16, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 37 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 345) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C) `ZINC000408074296.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074296 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 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, 3, 19, 22, 32, 32, 32, 32, 32, 32, 32, 31, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 41 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074296 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074296 Building ZINC000408074297 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074297 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/346 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 24, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 49 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/347 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 21, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 44 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/348 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/348' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 24, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 49 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/349 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/349' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 21, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 44 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074297 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 Building ZINC000408074297 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074297 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 346) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 24, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 49 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 347) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 21, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 44 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 348) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 24, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 49 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 349) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 21, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 44 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074297 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 Building ZINC000408074297 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074297 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 346) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 24, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 49 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 347) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 21, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 44 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 348) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 24, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 49 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 349) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 21, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 44 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074297 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 Building ZINC000408074297 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074297 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 346) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 24, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 49 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 347) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 21, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 44 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 348) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 24, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 49 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 349) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C) `ZINC000408074297.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408074297 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 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] 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 21, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 44 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074297 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074297 Building ZINC000408074355 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074355 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/350 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/351 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 22, 22, 22, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/352 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/352' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/353 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/353' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 22, 22, 22, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074355 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 Building ZINC000408074355 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074355 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 350) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 351) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 22, 22, 22, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 352) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 353) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 22, 22, 22, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074355 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 Building ZINC000408074355 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074355 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 350) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 351) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 22, 22, 22, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 352) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 353) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 22, 22, 22, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074355 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 Building ZINC000408074355 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074355 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 350) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 351) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 22, 22, 22, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 352) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 353) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074355.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074355 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 22, 22, 22, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074355 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074355 Building ZINC000408074357 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074357 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/354 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 11, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/355 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 3, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 18, 18, 18, 18, 18, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/356 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/356' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 11, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/357 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/357' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 3, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 18, 18, 18, 18, 18, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074357 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 Building ZINC000408074357 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074357 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 354) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 11, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 355) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 3, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 18, 18, 18, 18, 18, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 356) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 11, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 357) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 3, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 18, 18, 18, 18, 18, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074357 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 Building ZINC000408074357 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074357 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 354) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 11, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 355) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 3, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 18, 18, 18, 18, 18, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 356) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 11, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 357) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 3, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 18, 18, 18, 18, 18, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074357 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 Building ZINC000408074357 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074357 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 354) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 11, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 355) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 3, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 18, 18, 18, 18, 18, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 356) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 11, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 357) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074357.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074357 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 3, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 18, 18, 18, 18, 18, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074357 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074357 Building ZINC000408074359 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074359 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/358 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/359 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 7, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/360 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/360' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/361 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/361' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 7, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074359 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 Building ZINC000408074359 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074359 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 358) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 359) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 7, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 360) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 361) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 7, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074359 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 Building ZINC000408074359 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074359 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 358) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 359) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 7, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 360) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 361) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 7, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074359 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 Building ZINC000408074359 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074359 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 358) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 359) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 7, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 360) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 361) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@@H]2C)cn1) `ZINC000408074359.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074359 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 7, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074359 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074359 Building ZINC000408074360 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074360 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/362 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 3, 7, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/363 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 4, 10, 12, 16, 16, 16, 16, 16, 16, 16, 15, 16, 16, 4, 4, 18, 18, 18, 18, 18, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/364 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/364' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 3, 7, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/365 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/365' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 4, 10, 12, 16, 16, 16, 16, 16, 16, 16, 15, 16, 16, 4, 4, 18, 18, 18, 18, 18, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074360 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 Building ZINC000408074360 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074360 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 362) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 3, 7, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 363) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 4, 10, 12, 16, 16, 16, 16, 16, 16, 16, 15, 16, 16, 4, 4, 18, 18, 18, 18, 18, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 364) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 3, 7, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 365) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 4, 10, 12, 16, 16, 16, 16, 16, 16, 16, 15, 16, 16, 4, 4, 18, 18, 18, 18, 18, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074360 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 Building ZINC000408074360 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074360 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 362) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 3, 7, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 363) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 4, 10, 12, 16, 16, 16, 16, 16, 16, 16, 15, 16, 16, 4, 4, 18, 18, 18, 18, 18, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 364) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 3, 7, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 365) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 4, 10, 12, 16, 16, 16, 16, 16, 16, 16, 15, 16, 16, 4, 4, 18, 18, 18, 18, 18, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074360 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 Building ZINC000408074360 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408074360 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 362) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 3, 7, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 363) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 4, 10, 12, 16, 16, 16, 16, 16, 16, 16, 15, 16, 16, 4, 4, 18, 18, 18, 18, 18, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 364) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 3, 7, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 365) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H](C)N(C)C[C@H]2C)cn1) `ZINC000408074360.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408074360 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)N(C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 4, 10, 12, 16, 16, 16, 16, 16, 16, 16, 15, 16, 16, 4, 4, 18, 18, 18, 18, 18, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408074360 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408074360 Building ZINC000378487886 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378487886 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/366 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@H]2CCCC2=O)cn1) `ZINC000378487886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378487886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487886 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 17, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/367 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@H]2CCCC2=O)cn1) `ZINC000378487886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378487886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487886 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 18, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378487886 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 Building ZINC000378487886 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378487886 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 366) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@H]2CCCC2=O)cn1) `ZINC000378487886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378487886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487886 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 17, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 367) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@H]2CCCC2=O)cn1) `ZINC000378487886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378487886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487886 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 18, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378487886 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487886 Building ZINC000378487887 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378487887 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/368 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@@H]2CCCC2=O)cn1) `ZINC000378487887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378487887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487887 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 18, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/369 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@@H]2CCCC2=O)cn1) `ZINC000378487887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378487887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487887 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 17, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378487887 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 Building ZINC000378487887 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378487887 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 368) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@@H]2CCCC2=O)cn1) `ZINC000378487887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378487887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487887 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 18, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 369) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@@H]2CCCC2=O)cn1) `ZINC000378487887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378487887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487887 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 17, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378487887 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487887 Building ZINC000378487888 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378487888 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/370 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@@H]2CCCC2=O)cn1) `ZINC000378487888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378487888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487888 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 18, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 26, 9] 44 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/371 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@@H]2CCCC2=O)cn1) `ZINC000378487888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378487888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487888 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 19, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378487888 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 Building ZINC000378487888 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378487888 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 370) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@@H]2CCCC2=O)cn1) `ZINC000378487888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378487888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487888 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 18, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 26, 9] 44 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 371) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@@H]2CCCC2=O)cn1) `ZINC000378487888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378487888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487888 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2[C@@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 19, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378487888 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487888 Building ZINC000378487889 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378487889 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/372 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@H]2CCCC2=O)cn1) `ZINC000378487889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378487889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487889 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 20, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 70 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/373 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@H]2CCCC2=O)cn1) `ZINC000378487889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378487889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487889 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 18, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 25, 25, 25, 25, 25, 25, 9] 42 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 69 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378487889 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 Building ZINC000378487889 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378487889 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 372) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@H]2CCCC2=O)cn1) `ZINC000378487889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378487889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487889 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 20, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 70 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 373) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@H]2CCCC2=O)cn1) `ZINC000378487889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378487889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000378487889 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2[C@H]2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 18, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 25, 25, 25, 25, 25, 25, 9] 42 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 69 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378487889 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378487889 Building ZINC000339176925 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339176925 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/374 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCCC(N)=O)cn1) `ZINC000339176925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339176925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000339176925 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCCC(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 12, 21, 23, 23, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 2, 14, 14, 16, 16, 18, 19, 23, 23, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/375 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCCC(N)=O)cn1) `ZINC000339176925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339176925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000339176925 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCCC(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 12, 23, 26, 26, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 2, 14, 14, 16, 16, 21, 20, 26, 26, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000339176925 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 Building ZINC000339176925 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339176925 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 374) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)n1cc([C@@]([O-])([SiH3])C(=O)NCCCC(N)=O)cn1) `ZINC000339176925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339176925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000339176925 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCCC(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 12, 21, 23, 23, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 2, 14, 14, 16, 16, 18, 19, 23, 23, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 375) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)n1cc([C@]([O-])([SiH3])C(=O)NCCCC(N)=O)cn1) `ZINC000339176925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339176925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000339176925 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCCC(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 12, 23, 26, 26, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 2, 14, 14, 16, 16, 21, 20, 26, 26, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000339176925 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000339176925 Building ZINC000378574481 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378574481 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/376 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000378574481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378574481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000378574481 none COC(=O)[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 16, 13, 2, 13, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/377 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000378574481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378574481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000378574481 none COC(=O)[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 14, 14, 14, 14, 14, 14, 14, 13, 2, 13, 1, 1, 1, 5, 5, 5, 5, 5, 29, 29, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378574481 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 Building ZINC000378574481 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378574481 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 376) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC(=O)[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000378574481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378574481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000378574481 none COC(=O)[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 16, 13, 2, 13, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 377) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC(=O)[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000378574481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378574481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000378574481 none COC(=O)[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 14, 14, 14, 14, 14, 14, 14, 13, 2, 13, 1, 1, 1, 5, 5, 5, 5, 5, 29, 29, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378574481 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574481 Building ZINC000378574482 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378574482 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/378 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000378574482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378574482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000378574482 none COC(=O)[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 28, 13, 13, 13, 13, 13, 13, 13, 12, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 28, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/379 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000378574482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378574482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000378574482 none COC(=O)[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 17, 28, 17, 17, 17, 17, 17, 17, 17, 16, 2, 16, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 28, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378574482 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 Building ZINC000378574482 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000378574482 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 378) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC(=O)[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000378574482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000378574482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000378574482 none COC(=O)[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 28, 13, 13, 13, 13, 13, 13, 13, 12, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 28, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 379) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC(=O)[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000378574482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000378574482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000378574482 none COC(=O)[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 17, 28, 17, 17, 17, 17, 17, 17, 17, 16, 2, 16, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 28, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000378574482 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000378574482 Building ZINC000653320602 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000653320602 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/380 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CC(=O)O)cn1) `ZINC000653320602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000653320602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000653320602 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 25, 34, 34, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 25, 25, 102, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 226 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/381 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CC(=O)O)cn1) `ZINC000653320602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000653320602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000653320602 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 19, 27, 27, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 81, 7] 123 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 184 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000653320602 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 Building ZINC000653320602 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000653320602 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 380) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CC(=O)O)cn1) `ZINC000653320602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000653320602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000653320602 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 25, 34, 34, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 25, 25, 102, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 226 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 381) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CC(=O)O)cn1) `ZINC000653320602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000653320602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000653320602 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 19, 27, 27, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 81, 7] 123 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 184 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000653320602 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320602 Building ZINC000653320603 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000653320603 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/382 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CC(=O)O)cn1) `ZINC000653320603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000653320603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000653320603 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 19, 27, 27, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 81, 9] 120 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 182 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/383 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CC(=O)O)cn1) `ZINC000653320603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000653320603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000653320603 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 23, 30, 30, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 90, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 209 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000653320603 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 Building ZINC000653320603 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000653320603 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 382) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CC(=O)O)cn1) `ZINC000653320603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000653320603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000653320603 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 19, 27, 27, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 81, 9] 120 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 182 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 383) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CC(=O)O)cn1) `ZINC000653320603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000653320603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000653320603 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CC(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 23, 30, 30, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 90, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 209 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000653320603 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000653320603 Building ZINC000363909199 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000363909199 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/384 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(n2cncn2)C1) `ZINC000363909199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000363909199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000363909199 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(n2cncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 9, 9, 9, 41, 41, 41, 41, 9, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 41, 41, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/385 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(n2cncn2)C1) `ZINC000363909199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000363909199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000363909199 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(n2cncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 5, 5, 10, 10, 10, 42, 42, 42, 42, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 42, 42, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000363909199 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 Building ZINC000363909199 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000363909199 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 384) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(n2cncn2)C1) `ZINC000363909199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000363909199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000363909199 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(n2cncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 9, 9, 9, 41, 41, 41, 41, 9, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 41, 41, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 385) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(n2cncn2)C1) `ZINC000363909199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000363909199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000363909199 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(n2cncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 5, 5, 10, 10, 10, 42, 42, 42, 42, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 42, 42, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000363909199 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000363909199 Building ZINC000613727295 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613727295 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/386 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/386' -> `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)Nc1c[nH]ccc1=O) `ZINC000613727295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613727295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613727295 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c[nH]ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 30, 30, 30] 35 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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: 56 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/387 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/387' -> `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)Nc1c[nH]ccc1=O) `ZINC000613727295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613727295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613727295 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c[nH]ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 29, 29, 28, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 29, 29, 29] 35 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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: 56 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613727295 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 Building ZINC000613727295 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613727295 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 386) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c[nH]ccc1=O) `ZINC000613727295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613727295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613727295 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c[nH]ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 30, 30, 30] 35 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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: 56 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 387) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c[nH]ccc1=O) `ZINC000613727295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613727295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613727295 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c[nH]ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 29, 29, 28, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 29, 29, 29] 35 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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: 56 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613727295 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613727295 Building ZINC000652017579 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652017579 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/388 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652017579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652017579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000652017579 none O=C(N1CCO[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 9, 9, 9] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/389 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652017579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652017579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000652017579 none O=C(N1CCO[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 9, 9, 9] 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]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652017579 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 Building ZINC000652017579 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652017579 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 388) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(N1CCO[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652017579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652017579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000652017579 none O=C(N1CCO[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 9, 9, 9] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 389) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(N1CCO[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652017579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652017579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000652017579 none O=C(N1CCO[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 9, 9, 9] 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]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652017579 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017579 Building ZINC000652017583 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652017583 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/390 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652017583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652017583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000652017583 none O=C(N1CCO[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 10, 10, 10] 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/391 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652017583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652017583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000652017583 none O=C(N1CCO[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 11, 11, 11] 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]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652017583 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 Building ZINC000652017583 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652017583 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 390) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652017583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652017583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000652017583 none O=C(N1CCO[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 10, 10, 10] 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 391) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000652017583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652017583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000652017583 none O=C(N1CCO[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 11, 11, 11] 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]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652017583 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652017583 Building ZINC000182241955 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182241955 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/392 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)n1) `ZINC000182241955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182241955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000182241955 none CCc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 28, 7, 4, 21, 21, 21, 21, 21, 4, 7, 28, 28, 28, 28, 28, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/393 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)n1) `ZINC000182241955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182241955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000182241955 none CCc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 28, 7, 4, 21, 21, 21, 21, 21, 4, 7, 28, 28, 28, 28, 28, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000182241955 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 Building ZINC000182241955 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182241955 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 392) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)n1) `ZINC000182241955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182241955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000182241955 none CCc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 28, 7, 4, 21, 21, 21, 21, 21, 4, 7, 28, 28, 28, 28, 28, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 393) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)n1) `ZINC000182241955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182241955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000182241955 none CCc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 28, 7, 4, 21, 21, 21, 21, 21, 4, 7, 28, 28, 28, 28, 28, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000182241955 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000182241955 Building ZINC000185804324 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185804324 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/394 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ccnn1C) `ZINC000185804324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185804324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000185804324 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 1, 1, 1, 1, 5, 5, 5, 19, 31, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 5, 19, 19, 31, 31, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/395 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ccnn1C) `ZINC000185804324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185804324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000185804324 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 1, 1, 1, 1, 5, 5, 5, 19, 31, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 5, 19, 19, 31, 31, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000185804324 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 Building ZINC000185804324 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185804324 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 394) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ccnn1C) `ZINC000185804324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185804324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000185804324 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 1, 1, 1, 1, 5, 5, 5, 19, 31, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 5, 19, 19, 31, 31, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 395) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ccnn1C) `ZINC000185804324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185804324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000185804324 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 1, 1, 1, 1, 5, 5, 5, 19, 31, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 5, 19, 19, 31, 31, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000185804324 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000185804324 Building ZINC000408085637 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408085637 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/396 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C)COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408085637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408085637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000408085637 none CC[C@]1(C)COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 21, 10, 2, 16, 1, 1, 1, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 9, 9, 9] 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]) total number of confs: 85 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/397 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C)COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408085637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408085637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000408085637 none CC[C@]1(C)COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 18, 18, 18, 18, 18, 18, 18, 10, 2, 15, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8] 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]) total number of confs: 92 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408085637 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 Building ZINC000408085637 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408085637 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 396) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C)COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408085637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408085637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000408085637 none CC[C@]1(C)COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 21, 10, 2, 16, 1, 1, 1, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 9, 9, 9] 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]) total number of confs: 85 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 397) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C)COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408085637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408085637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000408085637 none CC[C@]1(C)COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 18, 18, 18, 18, 18, 18, 18, 10, 2, 15, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8] 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]) total number of confs: 92 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408085637 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085637 Building ZINC000408085638 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408085638 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/398 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C)COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408085638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408085638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000408085638 none CC[C@@]1(C)COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 18, 18, 18, 18, 18, 18, 18, 10, 2, 15, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8] 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]) total number of confs: 92 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/399 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C)COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408085638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408085638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000408085638 none CC[C@@]1(C)COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 9, 2, 15, 1, 1, 1, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9] 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]) total number of confs: 89 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408085638 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 Building ZINC000408085638 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408085638 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 398) grep: /scratch/xiaobo/170854/xdl-8058088.90/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@@]1(C)COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408085638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408085638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000408085638 none CC[C@@]1(C)COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 18, 18, 18, 18, 18, 18, 18, 10, 2, 15, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8] 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]) total number of confs: 92 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 399) grep: /scratch/xiaobo/170854/xdl-8058088.90/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@@]1(C)COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000408085638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408085638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000408085638 none CC[C@@]1(C)COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 9, 2, 15, 1, 1, 1, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9] 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]) total number of confs: 89 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408085638 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408085638 Building ZINC000186151370 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186151370 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/400 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C(F)(F)F)cn1) `ZINC000186151370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186151370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000186151370 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C(F)(F)F)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', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 4, 4, 4, 1, 1, 1, 1, 2, 2, 6, 6, 14, 19, 19, 19, 19, 19, 19, 4, 4, 17, 17, 17, 17, 17, 4, 6, 6, 6, 14, 14, 57, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 192 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/401 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C(F)(F)F)cn1) `ZINC000186151370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186151370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000186151370 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C(F)(F)F)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', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 2, 7, 7, 15, 21, 21, 21, 21, 21, 21, 5, 5, 16, 16, 16, 16, 16, 5, 7, 7, 7, 15, 15, 63, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 198 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000186151370 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 Building ZINC000186151370 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186151370 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 400) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C(F)(F)F)cn1) `ZINC000186151370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186151370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000186151370 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C(F)(F)F)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', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 4, 4, 4, 1, 1, 1, 1, 2, 2, 6, 6, 14, 19, 19, 19, 19, 19, 19, 4, 4, 17, 17, 17, 17, 17, 4, 6, 6, 6, 14, 14, 57, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 192 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 401) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C(F)(F)F)cn1) `ZINC000186151370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186151370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000186151370 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C(F)(F)F)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', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 2, 7, 7, 15, 21, 21, 21, 21, 21, 21, 5, 5, 16, 16, 16, 16, 16, 5, 7, 7, 7, 15, 15, 63, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 198 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000186151370 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000186151370 Building ZINC000893287024 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000893287024 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/402 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)c2nccnc2C)cn1) `ZINC000893287024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000893287024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000893287024 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)c2nccnc2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 5, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 16, 16, 16, 16, 16, 16, 6, 6, 18, 18, 18, 18, 18, 6, 7, 7, 7, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/403 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)c2nccnc2C)cn1) `ZINC000893287024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000893287024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000893287024 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)c2nccnc2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 5, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 16, 16, 16, 16, 16, 16, 6, 6, 17, 17, 17, 17, 17, 6, 7, 7, 7, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000893287024 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 Building ZINC000893287024 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000893287024 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 402) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)c2nccnc2C)cn1) `ZINC000893287024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000893287024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000893287024 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)c2nccnc2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 5, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 16, 16, 16, 16, 16, 16, 6, 6, 18, 18, 18, 18, 18, 6, 7, 7, 7, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 403) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)c2nccnc2C)cn1) `ZINC000893287024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000893287024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000893287024 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)c2nccnc2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 5, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 16, 16, 16, 16, 16, 16, 6, 6, 17, 17, 17, 17, 17, 6, 7, 7, 7, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000893287024 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893287024 Building ZINC000893289237 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000893289237 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/404 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccnc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000893289237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000893289237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000893289237 none Cc1nccnc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 11, 5, 11, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 11, 11, 11, 9, 9, 9, 9, 9] 38 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]) total number of confs: 51 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/405 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccnc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000893289237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000893289237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000893289237 none Cc1nccnc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 11, 5, 11, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 11, 11, 11, 10, 10, 10, 10, 10] 41 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]) total number of confs: 52 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000893289237 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 Building ZINC000893289237 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000893289237 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 404) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccnc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000893289237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000893289237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000893289237 none Cc1nccnc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 11, 5, 11, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 11, 11, 11, 9, 9, 9, 9, 9] 38 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]) total number of confs: 51 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 405) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccnc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000893289237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000893289237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000893289237 none Cc1nccnc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 11, 5, 11, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 11, 11, 11, 10, 10, 10, 10, 10] 41 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]) total number of confs: 52 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000893289237 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893289237 Building ZINC000893291442 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000893291442 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/406 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/406' -> `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)c1nccnc1C) `ZINC000893291442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000893291442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000893291442 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1nccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 15, 15, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 29, 29, 29, 29, 29] 39 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/407 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/407' -> `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)c1nccnc1C) `ZINC000893291442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000893291442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000893291442 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1nccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 16, 16, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 30, 30, 30, 30, 30] 36 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000893291442 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 Building ZINC000893291442 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000893291442 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 406) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1nccnc1C) `ZINC000893291442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000893291442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000893291442 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1nccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 15, 15, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 29, 29, 29, 29, 29] 39 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 407) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1nccnc1C) `ZINC000893291442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000893291442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000893291442 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1nccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 16, 16, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 30, 30, 30, 30, 30] 36 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000893291442 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893291442 Building ZINC000417183069 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000417183069 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/408 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 5, 5, 5, 5, 5, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/409 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/410 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/410' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 5, 5, 5, 5, 5, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/411 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/411' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000417183069 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 Building ZINC000417183069 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000417183069 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 408) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 5, 5, 5, 5, 5, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 409) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 410) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 5, 5, 5, 5, 5, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 411) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000417183069 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 Building ZINC000417183069 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000417183069 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 408) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 5, 5, 5, 5, 5, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 409) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 410) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 5, 5, 5, 5, 5, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 411) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000417183069 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 Building ZINC000417183069 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000417183069 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 408) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 5, 5, 5, 5, 5, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 409) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 410) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 5, 5, 5, 5, 5, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 411) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000417183069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183069 none O=C(N[C@@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000417183069 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183069 Building ZINC000417183070 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000417183070 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/412 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/413 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 4, 4, 4] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/414 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/414' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/415 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/415' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 4, 4, 4] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000417183070 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 Building ZINC000417183070 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000417183070 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 412) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 413) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 4, 4, 4] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 414) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 415) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 4, 4, 4] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000417183070 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 Building ZINC000417183070 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000417183070 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 412) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 413) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 4, 4, 4] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 414) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 415) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 4, 4, 4] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000417183070 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 Building ZINC000417183070 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000417183070 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 412) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 413) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 4, 4, 4] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 414) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 16, 16, 16, 16, 32, 39, 39, 16, 1, 1, 1, 4, 4, 4, 4, 4, 2, 16, 16, 16, 16, 32, 32, 39, 16, 16, 4, 4, 4] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 415) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000417183070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000417183070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000417183070 none O=C(N[C@H]1CCN(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 10, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 19, 19, 19, 19, 34, 41, 41, 19, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 19, 19, 34, 34, 41, 19, 19, 4, 4, 4] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000417183070 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000417183070 Building ZINC000497244430 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497244430 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/416 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000497244430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497244430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000497244430 none COC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 31, 48, 23, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 31, 23, 23, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/417 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000497244430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497244430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000497244430 none COC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 31, 48, 22, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 31, 22, 22, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000497244430 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 Building ZINC000497244430 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497244430 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 416) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000497244430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497244430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000497244430 none COC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 31, 48, 23, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 31, 23, 23, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 417) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000497244430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497244430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000497244430 none COC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 31, 48, 22, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 31, 22, 22, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000497244430 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000497244430 Building ZINC001353631140 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001353631140 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/418 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@@H]1CO)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001353631140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001353631140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001353631140 none O=C(N1CCSC[C@@H]1CO)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [18, 2, 18, 24, 24, 24, 24, 24, 24, 24, 44, 1, 1, 1, 5, 5, 1, 5, 5, 5, 24, 24, 24, 24, 24, 24, 44, 44, 132, 5, 5, 10, 5, 5] 300 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]) total number of confs: 312 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/419 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@@H]1CO)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001353631140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001353631140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001353631140 none O=C(N1CCSC[C@@H]1CO)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [16, 2, 16, 25, 25, 25, 25, 25, 25, 25, 45, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 25, 25, 25, 25, 45, 45, 135, 5, 5, 10, 5, 5] 300 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]) total number of confs: 304 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001353631140 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 Building ZINC001353631140 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001353631140 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 418) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@@H]1CO)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001353631140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001353631140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001353631140 none O=C(N1CCSC[C@@H]1CO)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [18, 2, 18, 24, 24, 24, 24, 24, 24, 24, 44, 1, 1, 1, 5, 5, 1, 5, 5, 5, 24, 24, 24, 24, 24, 24, 44, 44, 132, 5, 5, 10, 5, 5] 300 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]) total number of confs: 312 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 419) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@@H]1CO)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001353631140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001353631140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001353631140 none O=C(N1CCSC[C@@H]1CO)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [16, 2, 16, 25, 25, 25, 25, 25, 25, 25, 45, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 25, 25, 25, 25, 45, 45, 135, 5, 5, 10, 5, 5] 300 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]) total number of confs: 304 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001353631140 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631140 Building ZINC001353631141 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001353631141 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/420 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@H]1CO)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001353631141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001353631141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001353631141 none O=C(N1CCSC[C@H]1CO)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 17, 22, 22, 22, 22, 22, 22, 22, 46, 1, 1, 1, 5, 5, 1, 1, 5, 5, 22, 22, 22, 22, 22, 22, 46, 46, 138, 5, 5, 10, 5, 5] 300 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]) total number of confs: 323 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/421 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@H]1CO)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001353631141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001353631141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001353631141 none O=C(N1CCSC[C@H]1CO)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 17, 28, 28, 28, 28, 28, 28, 28, 45, 1, 1, 1, 5, 5, 1, 2, 5, 5, 28, 28, 28, 28, 28, 28, 45, 45, 135, 5, 5, 10, 5, 5] 300 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]) total number of confs: 299 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001353631141 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 Building ZINC001353631141 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001353631141 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 420) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@H]1CO)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001353631141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001353631141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001353631141 none O=C(N1CCSC[C@H]1CO)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 17, 22, 22, 22, 22, 22, 22, 22, 46, 1, 1, 1, 5, 5, 1, 1, 5, 5, 22, 22, 22, 22, 22, 22, 46, 46, 138, 5, 5, 10, 5, 5] 300 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]) total number of confs: 323 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 421) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@H]1CO)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001353631141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001353631141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001353631141 none O=C(N1CCSC[C@H]1CO)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 17, 28, 28, 28, 28, 28, 28, 28, 45, 1, 1, 1, 5, 5, 1, 2, 5, 5, 28, 28, 28, 28, 28, 28, 45, 45, 135, 5, 5, 10, 5, 5] 300 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]) total number of confs: 299 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001353631141 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001353631141 Building ZINC000641752105 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641752105 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/422 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(OCC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000641752105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641752105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000641752105 none O=C(N1CC(OCC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 20, 30, 43, 43, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 30, 30, 43, 6, 6, 3, 3, 3] 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/423 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(OCC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000641752105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641752105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000641752105 none O=C(N1CC(OCC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 20, 30, 43, 43, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 30, 30, 43, 6, 6, 3, 3, 3] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000641752105 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 Building ZINC000641752105 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641752105 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 422) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(OCC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000641752105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641752105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000641752105 none O=C(N1CC(OCC(F)F)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 20, 30, 43, 43, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 30, 30, 43, 6, 6, 3, 3, 3] 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 423) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(OCC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000641752105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641752105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000641752105 none O=C(N1CC(OCC(F)F)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 8, 6, 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, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 20, 30, 43, 43, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 30, 30, 43, 6, 6, 3, 3, 3] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000641752105 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000641752105 Building ZINC000628526744 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000628526744 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/424 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)[C@@H](O)C2)cc1Cl) `ZINC000628526744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628526744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000628526744 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)[C@@H](O)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', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 14, 14, 42, 42, 14, 14, 6] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/425 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)[C@@H](O)C2)cc1Cl) `ZINC000628526744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628526744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000628526744 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)[C@@H](O)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', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 14, 14, 14, 6, 6, 14, 14, 42, 42, 14, 14, 6] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000628526744 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 Building ZINC000628526744 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000628526744 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 424) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)[C@@H](O)C2)cc1Cl) `ZINC000628526744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628526744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000628526744 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)[C@@H](O)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', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 14, 14, 42, 42, 14, 14, 6] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 425) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)[C@@H](O)C2)cc1Cl) `ZINC000628526744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628526744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000628526744 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)[C@@H](O)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', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 14, 14, 14, 6, 6, 14, 14, 42, 42, 14, 14, 6] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000628526744 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000628526744 Building ZINC000584780485 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584780485 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/426 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/426' -> `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]1CO[C@@H](C)C1) `ZINC000584780485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584780485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780485 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CO[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 108 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/427 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/427' -> `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]1CO[C@@H](C)C1) `ZINC000584780485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584780485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780485 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CO[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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 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, 5, 5, 1, 1, 1, 1, 9, 9, 15, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 40, 40, 40, 40, 40, 40, 40] 48 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584780485 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 Building ZINC000584780485 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584780485 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 426) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CO[C@@H](C)C1) `ZINC000584780485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584780485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780485 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CO[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 108 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 427) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CO[C@@H](C)C1) `ZINC000584780485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584780485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780485 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CO[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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 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, 5, 5, 1, 1, 1, 1, 9, 9, 15, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 40, 40, 40, 40, 40, 40, 40] 48 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584780485 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780485 Building ZINC000584780486 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584780486 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/428 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/428' -> `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]1CO[C@H](C)C1) `ZINC000584780486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584780486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780486 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 16, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/429 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/429' -> `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]1CO[C@H](C)C1) `ZINC000584780486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584780486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780486 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 17, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584780486 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 Building ZINC000584780486 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584780486 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 428) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@H](C)C1) `ZINC000584780486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584780486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780486 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 16, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 429) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@H](C)C1) `ZINC000584780486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584780486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780486 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 17, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584780486 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780486 Building ZINC000584780487 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584780487 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/430 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/430' -> `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]1CO[C@@H](C)C1) `ZINC000584780487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584780487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780487 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 19, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/431 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/431' -> `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]1CO[C@@H](C)C1) `ZINC000584780487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584780487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780487 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584780487 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 Building ZINC000584780487 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584780487 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 430) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@@H](C)C1) `ZINC000584780487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584780487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780487 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 19, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 431) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@@H](C)C1) `ZINC000584780487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584780487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780487 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CO[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584780487 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780487 Building ZINC000584780482 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584780482 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/432 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/432' -> `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]1CO[C@H](C)C1) `ZINC000584780482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584780482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780482 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CO[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 17, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/433 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/433' -> `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]1CO[C@H](C)C1) `ZINC000584780482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584780482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780482 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CO[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 19, 41, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 41, 41, 41, 41, 41, 41, 41] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584780482 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 Building ZINC000584780482 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584780482 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 432) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CO[C@H](C)C1) `ZINC000584780482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584780482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780482 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CO[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 17, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 433) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CO[C@H](C)C1) `ZINC000584780482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584780482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000584780482 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CO[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 19, 41, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 41, 41, 41, 41, 41, 41, 41] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000584780482 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000584780482 Building ZINC000576226025 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000576226025 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/434 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H]1N) `ZINC000576226025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000576226025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000576226025 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/435 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H]1N) `ZINC000576226025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000576226025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000576226025 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000576226025 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 Building ZINC000576226025 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000576226025 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 434) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H]1N) `ZINC000576226025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000576226025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000576226025 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 435) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H]1N) `ZINC000576226025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000576226025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000576226025 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000576226025 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000576226025 Building ZINC000408089512 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408089512 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/436 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/436' -> `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@@]1(C)CCCOC1) `ZINC000408089512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408089512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408089512 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 19, 44, 44, 44, 44, 44, 38, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/437 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/437' -> `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@@]1(C)CCCOC1) `ZINC000408089512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408089512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408089512 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 19, 43, 43, 43, 43, 43, 36, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 153 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408089512 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 Building ZINC000408089512 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408089512 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 436) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCCOC1) `ZINC000408089512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408089512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408089512 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 19, 44, 44, 44, 44, 44, 38, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 437) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCCOC1) `ZINC000408089512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408089512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408089512 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 19, 43, 43, 43, 43, 43, 36, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 153 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408089512 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089512 Building ZINC000408089513 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408089513 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/438 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/438' -> `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@]1(C)CCCOC1) `ZINC000408089513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408089513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408089513 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 25, 43, 43, 43, 43, 43, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 134 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/439 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/439' -> `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@]1(C)CCCOC1) `ZINC000408089513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408089513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408089513 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 22, 41, 41, 41, 41, 41, 38, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 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]) total number of confs: 123 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408089513 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 Building ZINC000408089513 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408089513 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 438) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCCOC1) `ZINC000408089513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408089513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408089513 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 25, 43, 43, 43, 43, 43, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 134 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 439) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCCOC1) `ZINC000408089513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408089513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408089513 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 22, 41, 41, 41, 41, 41, 38, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 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]) total number of confs: 123 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408089513 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408089513 Building ZINC000364143477 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000364143477 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/440 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC3(CCNCC3)C2)cn1) `ZINC000364143477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000364143477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000364143477 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC3(CCNCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 13, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/441 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC3(CCNCC3)C2)cn1) `ZINC000364143477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000364143477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000364143477 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC3(CCNCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 10, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000364143477 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 Building ZINC000364143477 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000364143477 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 440) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC3(CCNCC3)C2)cn1) `ZINC000364143477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000364143477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000364143477 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC3(CCNCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 13, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 441) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC3(CCNCC3)C2)cn1) `ZINC000364143477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000364143477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000364143477 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCC3(CCNCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 10, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000364143477 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000364143477 Building ZINC000119635653 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119635653 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/442 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(C)(C)C2)cn1) `ZINC000119635653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119635653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000119635653 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 9, 10, 16, 16, 16, 16, 16, 16, 16, 4, 4, 17, 17, 17, 17, 17, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/443 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(C)(C)C2)cn1) `ZINC000119635653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119635653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000119635653 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 9, 11, 15, 15, 15, 15, 15, 15, 15, 6, 6, 19, 19, 19, 19, 19, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000119635653 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 Building ZINC000119635653 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119635653 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 442) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(C)(C)C2)cn1) `ZINC000119635653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119635653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000119635653 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 9, 10, 16, 16, 16, 16, 16, 16, 16, 4, 4, 17, 17, 17, 17, 17, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 443) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(C)(C)C2)cn1) `ZINC000119635653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119635653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000119635653 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 9, 11, 15, 15, 15, 15, 15, 15, 15, 6, 6, 19, 19, 19, 19, 19, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000119635653 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119635653 Building ZINC001699397751 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001699397751 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/444 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001699397751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001699397751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001699397751 none CCN1CC[C@H](NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 35, 27, 35, 14, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 21, 14, 14, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/445 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001699397751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001699397751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001699397751 none CCN1CC[C@H](NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 26, 39, 14, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50, 50, 50, 50, 39, 39, 39, 39, 20, 14, 14, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001699397751 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 Building ZINC001699397751 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001699397751 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 444) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN1CC[C@H](NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001699397751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001699397751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001699397751 none CCN1CC[C@H](NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 35, 27, 35, 14, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 21, 14, 14, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 445) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN1CC[C@H](NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001699397751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001699397751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001699397751 none CCN1CC[C@H](NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 26, 39, 14, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50, 50, 50, 50, 39, 39, 39, 39, 20, 14, 14, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001699397751 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397751 Building ZINC001699397757 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001699397757 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/446 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001699397757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001699397757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001699397757 none CCN1CC[C@@H](NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 31, 32, 18, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 32, 32, 32, 32, 25, 18, 18, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/447 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001699397757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001699397757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001699397757 none CCN1CC[C@@H](NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 32, 33, 20, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 33, 33, 33, 33, 29, 20, 20, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001699397757 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 Building ZINC001699397757 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001699397757 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 446) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN1CC[C@@H](NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001699397757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001699397757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001699397757 none CCN1CC[C@@H](NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 31, 32, 18, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 32, 32, 32, 32, 25, 18, 18, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 447) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN1CC[C@@H](NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001699397757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001699397757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001699397757 none CCN1CC[C@@H](NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 32, 33, 20, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 33, 33, 33, 33, 29, 20, 20, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001699397757 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001699397757 Building ZINC000408091554 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091554 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/448 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/449 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/450 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/450' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/451 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/451' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091554 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 Building ZINC000408091554 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091554 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 448) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 449) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 450) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 451) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091554 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 Building ZINC000408091554 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091554 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 448) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 449) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 450) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 451) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091554 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 Building ZINC000408091554 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091554 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 448) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 449) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 450) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 451) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1) `ZINC000408091554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091554 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091554 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091554 Building ZINC000408091556 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091556 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/452 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 29, 29, 29, 29, 29, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/453 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 26, 26, 26, 26, 26, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/454 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/454' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 29, 29, 29, 29, 29, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/455 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/455' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 26, 26, 26, 26, 26, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091556 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 Building ZINC000408091556 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091556 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 452) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 29, 29, 29, 29, 29, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 453) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 26, 26, 26, 26, 26, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 454) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 29, 29, 29, 29, 29, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 455) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 26, 26, 26, 26, 26, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091556 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 Building ZINC000408091556 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091556 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 452) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 29, 29, 29, 29, 29, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 453) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 26, 26, 26, 26, 26, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 454) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 29, 29, 29, 29, 29, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 455) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 26, 26, 26, 26, 26, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091556 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 Building ZINC000408091556 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091556 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 452) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 29, 29, 29, 29, 29, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 453) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 26, 26, 26, 26, 26, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 454) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 29, 29, 29, 29, 29, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 455) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1) `ZINC000408091556.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091556 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 26, 26, 26, 26, 26, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091556 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091556 Building ZINC000408091557 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091557 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/456 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 10, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 19, 19, 19, 19, 19, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/457 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/458 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/458' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 10, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 19, 19, 19, 19, 19, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/459 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/459' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091557 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 Building ZINC000408091557 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091557 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 456) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 10, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 19, 19, 19, 19, 19, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 457) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 458) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 10, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 19, 19, 19, 19, 19, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 459) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091557 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 Building ZINC000408091557 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091557 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 456) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 10, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 19, 19, 19, 19, 19, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 457) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 458) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 10, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 19, 19, 19, 19, 19, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 459) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091557 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 Building ZINC000408091557 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091557 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 456) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 10, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 19, 19, 19, 19, 19, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 457) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 458) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 10, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 19, 19, 19, 19, 19, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 459) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1) `ZINC000408091557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091557 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091557 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091557 Building ZINC000408091558 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091558 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/460 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/461 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/462 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/462' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/463 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/463' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091558 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 Building ZINC000408091558 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091558 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 460) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 461) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 462) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 463) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091558 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 Building ZINC000408091558 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091558 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 460) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 461) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 462) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 463) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091558 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 Building ZINC000408091558 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408091558 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 460) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 461) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 462) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 463) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1) `ZINC000408091558.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408091558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408091558 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408091558 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408091558 Building ZINC000855645917 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855645917 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/464 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)OCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000855645917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855645917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000855645917 none CN(C)C(=O)OCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 25, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 48, 25, 25, 15, 15, 3, 3, 3, 1, 3, 3] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/465 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)OCCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000855645917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855645917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000855645917 none CN(C)C(=O)OCCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 25, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 48, 25, 25, 15, 15, 3, 3, 3, 1, 3, 3] 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000855645917 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 Building ZINC000855645917 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855645917 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 464) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(C)C(=O)OCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000855645917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855645917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000855645917 none CN(C)C(=O)OCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 25, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 48, 25, 25, 15, 15, 3, 3, 3, 1, 3, 3] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 465) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(C)C(=O)OCCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000855645917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855645917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000855645917 none CN(C)C(=O)OCCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 25, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 48, 25, 25, 15, 15, 3, 3, 3, 1, 3, 3] 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000855645917 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000855645917 Building ZINC000429800176 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429800176 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/466 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nn[nH]n1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429800176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429800176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 23 natoms 22 natoms 21 natoms 20 names: ZINC000429800176 none O=C(Nc1nn[nH]n1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 14, 14, 14, 14, 14, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 25 rigid atoms, others: [1, 10, 11, 9] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/467 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nn[nH]n1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429800176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429800176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 23 natoms 22 natoms 21 natoms 20 names: ZINC000429800176 none O=C(Nc1nn[nH]n1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 14, 14, 14, 14, 14, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 25 rigid atoms, others: [1, 10, 11, 9] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000429800176 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 Building ZINC000429800176 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429800176 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 466) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nn[nH]n1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429800176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429800176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 23 natoms 22 natoms 21 natoms 20 names: ZINC000429800176 none O=C(Nc1nn[nH]n1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 14, 14, 14, 14, 14, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 25 rigid atoms, others: [1, 10, 11, 9] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 467) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nn[nH]n1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429800176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429800176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 23 natoms 22 natoms 21 natoms 20 names: ZINC000429800176 none O=C(Nc1nn[nH]n1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 14, 14, 14, 14, 14, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 25 rigid atoms, others: [1, 10, 11, 9] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000429800176 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000429800176 Building ZINC000582122460 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000582122460 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/468 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000582122460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000582122460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000582122460 none CC(=O)NCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 18, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 27, 27, 18, 18, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/469 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000582122460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000582122460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000582122460 none CC(=O)NCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 18, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 27, 27, 18, 18, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000582122460 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 Building ZINC000582122460 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000582122460 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 468) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)NCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000582122460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000582122460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000582122460 none CC(=O)NCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 18, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 27, 27, 18, 18, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 469) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)NCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000582122460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000582122460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000582122460 none CC(=O)NCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 18, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 27, 27, 18, 18, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000582122460 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000582122460 Building ZINC000652052041 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000652052041 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/470 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 15, 2, 16, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 29, 38, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 28, 28, 28, 28, 29, 29, 38, 38, 114] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 235 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/471 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 15, 2, 16, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 29, 38, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 28, 28, 28, 28, 29, 29, 38, 38, 114] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 235 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/472 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/472' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 17, 2, 18, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 27, 28, 32, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 27, 27, 27, 27, 28, 28, 32, 32, 96] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/473 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/473' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 17, 2, 18, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 27, 28, 32, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 27, 27, 27, 27, 28, 28, 32, 32, 96] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652052041 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 Building ZINC000652052041 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000652052041 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 470) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 15, 2, 16, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 29, 38, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 28, 28, 28, 28, 29, 29, 38, 38, 114] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 235 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 471) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 15, 2, 16, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 29, 38, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 28, 28, 28, 28, 29, 29, 38, 38, 114] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 235 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 472) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 17, 2, 18, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 27, 28, 32, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 27, 27, 27, 27, 28, 28, 32, 32, 96] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 473) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 17, 2, 18, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 27, 28, 32, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 27, 27, 27, 27, 28, 28, 32, 32, 96] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652052041 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 Building ZINC000652052041 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000652052041 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 470) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 15, 2, 16, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 29, 38, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 28, 28, 28, 28, 29, 29, 38, 38, 114] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 235 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 471) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 15, 2, 16, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 29, 38, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 28, 28, 28, 28, 29, 29, 38, 38, 114] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 235 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 472) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 17, 2, 18, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 27, 28, 32, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 27, 27, 27, 27, 28, 28, 32, 32, 96] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 473) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 17, 2, 18, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 27, 28, 32, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 27, 27, 27, 27, 28, 28, 32, 32, 96] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652052041 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 Building ZINC000652052041 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000652052041 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 470) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 15, 2, 16, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 29, 38, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 28, 28, 28, 28, 29, 29, 38, 38, 114] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 235 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 471) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 15, 2, 16, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 29, 38, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 28, 28, 28, 28, 29, 29, 38, 38, 114] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 235 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 472) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 17, 2, 18, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 27, 28, 32, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 27, 27, 27, 27, 28, 28, 32, 32, 96] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 473) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO) `ZINC000652052041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000652052041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000652052041 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCN1CCO 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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 17, 2, 18, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 27, 28, 32, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 27, 27, 27, 27, 28, 28, 32, 32, 96] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652052041 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652052041 Building ZINC000618998010 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618998010 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/474 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000618998010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618998010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000618998010 none CN1C[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 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] 0 hydrogens 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, 30, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 17, 17, 4, 3, 3, 1, 3, 3, 48, 48] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/475 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000618998010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618998010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000618998010 none CN1C[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 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] 0 hydrogens 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, 27, 45, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 18, 18, 4, 3, 3, 1, 3, 3, 45, 45] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000618998010 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 Building ZINC000618998010 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618998010 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 474) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN1C[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000618998010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618998010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000618998010 none CN1C[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 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] 0 hydrogens 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, 30, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 17, 17, 4, 3, 3, 1, 3, 3, 48, 48] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 475) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN1C[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000618998010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618998010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000618998010 none CN1C[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 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] 0 hydrogens 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, 27, 45, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 18, 18, 4, 3, 3, 1, 3, 3, 45, 45] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000618998010 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998010 Building ZINC000618998011 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618998011 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/476 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000618998011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618998011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000618998011 none CN1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 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] 0 hydrogens 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, 27, 45, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 18, 18, 4, 3, 3, 1, 3, 3, 45, 45] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/477 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000618998011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618998011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000618998011 none CN1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 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] 0 hydrogens 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, 30, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 17, 17, 4, 3, 3, 1, 3, 3, 48, 48] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000618998011 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 Building ZINC000618998011 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618998011 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 476) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000618998011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618998011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000618998011 none CN1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 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] 0 hydrogens 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, 27, 45, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 18, 18, 4, 3, 3, 1, 3, 3, 45, 45] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 477) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000618998011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618998011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000618998011 none CN1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 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] 0 hydrogens 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, 30, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 17, 17, 4, 3, 3, 1, 3, 3, 48, 48] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000618998011 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000618998011 Building ZINC000194258367 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194258367 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/478 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)OCCO2)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194258367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194258367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000194258367 none O=C(N1CCC2(C1)OCCO2)[C@]([O-])([SiH3])c1ccccc1 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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 10, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 1, 5, 5] 34 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/479 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)OCCO2)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194258367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194258367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000194258367 none O=C(N1CCC2(C1)OCCO2)[C@@]([O-])([SiH3])c1ccccc1 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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 10, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 1, 5, 5] 34 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194258367 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 Building ZINC000194258367 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194258367 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 478) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N1CCC2(C1)OCCO2)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194258367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194258367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000194258367 none O=C(N1CCC2(C1)OCCO2)[C@]([O-])([SiH3])c1ccccc1 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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 10, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 1, 5, 5] 34 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 479) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N1CCC2(C1)OCCO2)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194258367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194258367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000194258367 none O=C(N1CCC2(C1)OCCO2)[C@@]([O-])([SiH3])c1ccccc1 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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 10, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 1, 5, 5] 34 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194258367 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194258367 Building ZINC000194263501 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194263501 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/480 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194263501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194263501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194263501 none Cn1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 43, 32, 24, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 43, 43, 43, 129, 32, 32, 24, 24, 6, 4, 4, 1, 4, 4] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/481 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194263501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194263501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194263501 none Cn1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 33, 25, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 132, 33, 33, 25, 25, 6, 3, 3, 1, 3, 3] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194263501 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 Building ZINC000194263501 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194263501 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 480) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194263501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194263501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194263501 none Cn1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 43, 32, 24, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 43, 43, 43, 129, 32, 32, 24, 24, 6, 4, 4, 1, 4, 4] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 481) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194263501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194263501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194263501 none Cn1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 33, 25, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 132, 33, 33, 25, 25, 6, 3, 3, 1, 3, 3] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194263501 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194263501 Building ZINC001026738137 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001026738137 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/482 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNCc2cnon2)C1) `ZINC001026738137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001026738137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001026738137 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNCc2cnon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 8, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 11, 11, 11, 11, 11, 28, 36, 46, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 28, 28, 36, 46, 46, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/483 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNCc2cnon2)C1) `ZINC001026738137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001026738137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001026738137 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNCc2cnon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 8, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 23, 29, 41, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 23, 29, 41, 41, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001026738137 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 Building ZINC001026738137 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001026738137 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 482) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNCc2cnon2)C1) `ZINC001026738137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001026738137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001026738137 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNCc2cnon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 8, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 11, 11, 11, 11, 11, 28, 36, 46, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 28, 28, 36, 46, 46, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 483) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNCc2cnon2)C1) `ZINC001026738137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001026738137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001026738137 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNCc2cnon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 8, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 23, 29, 41, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 23, 29, 41, 41, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001026738137 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001026738137 Building ZINC000194540468 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194540468 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/484 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)n1) `ZINC000194540468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194540468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000194540468 none Nc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 3, 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] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 44, 44, 11, 11, 3, 3, 3, 1, 3, 3] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/485 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)n1) `ZINC000194540468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194540468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000194540468 none Nc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 3, 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] 0 hydrogens 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, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 44, 44, 12, 12, 3, 3, 3, 1, 3, 3] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194540468 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 Building ZINC000194540468 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194540468 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 484) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Nc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)n1) `ZINC000194540468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194540468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000194540468 none Nc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 3, 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] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 44, 44, 11, 11, 3, 3, 3, 1, 3, 3] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 485) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Nc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)n1) `ZINC000194540468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194540468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000194540468 none Nc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 3, 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] 0 hydrogens 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, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 44, 44, 12, 12, 3, 3, 3, 1, 3, 3] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194540468 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194540468 Building ZINC000194551756 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194551756 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/486 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccn[nH]1) `ZINC000194551756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194551756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194551756 none O=C(NCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccn[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 40, 49, 49, 49, 49, 49, 40, 26, 26, 17, 17, 4, 3, 3, 1, 3, 3, 49, 49] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/487 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccn[nH]1) `ZINC000194551756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194551756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194551756 none O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccn[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 40, 49, 49, 49, 49, 49, 40, 25, 25, 16, 16, 4, 3, 3, 1, 3, 3, 49, 49] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194551756 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 Building ZINC000194551756 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194551756 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 486) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(NCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccn[nH]1) `ZINC000194551756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194551756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194551756 none O=C(NCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccn[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 40, 49, 49, 49, 49, 49, 40, 26, 26, 17, 17, 4, 3, 3, 1, 3, 3, 49, 49] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 487) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccn[nH]1) `ZINC000194551756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194551756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194551756 none O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccn[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 40, 49, 49, 49, 49, 49, 40, 25, 25, 16, 16, 4, 3, 3, 1, 3, 3, 49, 49] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194551756 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194551756 Building ZINC000194575771 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194575771 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/488 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194575771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194575771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000194575771 none Cn1nccc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [45, 45, 45, 45, 45, 30, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 45, 45, 45, 45, 45, 30, 30, 18, 18, 4, 4, 4, 1, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/489 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194575771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194575771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000194575771 none Cn1nccc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [45, 45, 45, 45, 45, 29, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 45, 45, 45, 45, 45, 29, 29, 18, 18, 4, 4, 4, 1, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194575771 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 Building ZINC000194575771 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194575771 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 488) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1nccc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194575771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194575771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000194575771 none Cn1nccc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [45, 45, 45, 45, 45, 30, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 45, 45, 45, 45, 45, 30, 30, 18, 18, 4, 4, 4, 1, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 489) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1nccc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194575771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194575771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000194575771 none Cn1nccc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [45, 45, 45, 45, 45, 29, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 45, 45, 45, 45, 45, 29, 29, 18, 18, 4, 4, 4, 1, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194575771 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194575771 Building ZINC000194704652 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194704652 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/490 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1) `ZINC000194704652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194704652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704652 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 13, 30, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 13, 13, 30, 30, 90] 99 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 202 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/491 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1) `ZINC000194704652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194704652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704652 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 13, 13, 13, 13, 29, 13, 13, 13, 13, 13, 13, 6, 6, 1, 6, 6, 13, 13, 29, 29, 87] 99 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194704652 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 Building ZINC000194704652 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194704652 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 490) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1) `ZINC000194704652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194704652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704652 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 13, 30, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 13, 13, 30, 30, 90] 99 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 202 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 491) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1) `ZINC000194704652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194704652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704652 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 13, 13, 13, 13, 29, 13, 13, 13, 13, 13, 13, 6, 6, 1, 6, 6, 13, 13, 29, 29, 87] 99 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194704652 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704652 Building ZINC000194704670 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194704670 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/492 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1) `ZINC000194704670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194704670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704670 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 8, 2, 8, 1, 1, 1, 3, 3, 1, 3, 3, 26, 26, 26, 26, 47, 26, 26, 26, 26, 26, 26, 3, 3, 1, 3, 3, 26, 26, 47, 47, 141] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 301 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/493 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1) `ZINC000194704670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194704670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704670 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 11, 1, 11, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 48, 28, 28, 28, 28, 28, 28, 3, 3, 1, 3, 3, 28, 28, 48, 48, 144] 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]) total number of confs: 298 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194704670 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 Building ZINC000194704670 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194704670 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 492) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1) `ZINC000194704670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194704670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704670 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 8, 2, 8, 1, 1, 1, 3, 3, 1, 3, 3, 26, 26, 26, 26, 47, 26, 26, 26, 26, 26, 26, 3, 3, 1, 3, 3, 26, 26, 47, 47, 141] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 301 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 493) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1) `ZINC000194704670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194704670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704670 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 11, 1, 11, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 48, 28, 28, 28, 28, 28, 28, 3, 3, 1, 3, 3, 28, 28, 48, 48, 144] 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]) total number of confs: 298 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194704670 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704670 Building ZINC000194704682 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194704682 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/494 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1) `ZINC000194704682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194704682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704682 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 11, 1, 11, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 48, 28, 28, 28, 28, 28, 28, 3, 3, 1, 3, 3, 28, 28, 48, 48, 144] 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]) total number of confs: 297 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/495 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1) `ZINC000194704682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194704682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704682 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 8, 1, 8, 1, 1, 1, 3, 3, 1, 3, 3, 26, 26, 26, 26, 47, 26, 26, 26, 26, 26, 26, 3, 3, 1, 3, 3, 26, 26, 47, 47, 141] 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]) total number of confs: 299 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194704682 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 Building ZINC000194704682 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194704682 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 494) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1) `ZINC000194704682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194704682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704682 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 11, 1, 11, 1, 1, 1, 3, 3, 1, 3, 3, 28, 28, 28, 28, 48, 28, 28, 28, 28, 28, 28, 3, 3, 1, 3, 3, 28, 28, 48, 48, 144] 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]) total number of confs: 297 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 495) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1) `ZINC000194704682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194704682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704682 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 8, 1, 8, 1, 1, 1, 3, 3, 1, 3, 3, 26, 26, 26, 26, 47, 26, 26, 26, 26, 26, 26, 3, 3, 1, 3, 3, 26, 26, 47, 47, 141] 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]) total number of confs: 299 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194704682 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704682 Building ZINC000194704695 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194704695 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/496 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1) `ZINC000194704695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194704695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704695 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 15, 15, 15, 15, 41, 15, 15, 15, 15, 15, 15, 6, 6, 1, 6, 6, 15, 15, 41, 41, 123] 129 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]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/497 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1) `ZINC000194704695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194704695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704695 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 12, 12, 12, 12, 28, 12, 12, 12, 12, 12, 12, 5, 5, 1, 5, 5, 12, 12, 28, 28, 84] 105 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194704695 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 Building ZINC000194704695 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194704695 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 496) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1) `ZINC000194704695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194704695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704695 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 15, 15, 15, 15, 41, 15, 15, 15, 15, 15, 15, 6, 6, 1, 6, 6, 15, 15, 41, 41, 123] 129 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]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 497) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1) `ZINC000194704695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194704695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000194704695 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H](CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 12, 12, 12, 12, 28, 12, 12, 12, 12, 12, 12, 5, 5, 1, 5, 5, 12, 12, 28, 28, 84] 105 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000194704695 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000194704695 Building ZINC000759894642 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000759894642 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/498 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccsc2C(N)=O)cn1) `ZINC000759894642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000759894642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000759894642 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccsc2C(N)=O)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.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 1, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 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: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 6, 6, 12, 12, 12, 12, 12, 6, 3, 10, 10, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/499 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccsc2C(N)=O)cn1) `ZINC000759894642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000759894642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000759894642 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccsc2C(N)=O)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.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 1, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 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: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 6, 6, 12, 12, 12, 12, 12, 6, 3, 10, 10, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000759894642 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 Building ZINC000759894642 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000759894642 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 498) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccsc2C(N)=O)cn1) `ZINC000759894642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000759894642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000759894642 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccsc2C(N)=O)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.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 1, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 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: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 6, 6, 12, 12, 12, 12, 12, 6, 3, 10, 10, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 499) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccsc2C(N)=O)cn1) `ZINC000759894642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000759894642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000759894642 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccsc2C(N)=O)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.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 1, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 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: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 6, 6, 12, 12, 12, 12, 12, 6, 3, 10, 10, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000759894642 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000759894642 Building ZINC000195128338 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195128338 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/500 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000195128338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195128338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195128338 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 4, 13, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 16, 27, 27, 27, 27, 27, 13, 13, 13, 4, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27] 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]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/501 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000195128338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195128338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195128338 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 15, 27, 27, 27, 27, 27, 12, 12, 12, 4, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195128338 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 Building ZINC000195128338 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195128338 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 500) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000195128338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195128338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195128338 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 4, 13, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 16, 27, 27, 27, 27, 27, 13, 13, 13, 4, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27] 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]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 501) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000195128338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195128338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195128338 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 15, 27, 27, 27, 27, 27, 12, 12, 12, 4, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195128338 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195128338 Building ZINC000195156718 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195156718 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/502 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 34, 17, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 13, 13, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/503 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 34, 17, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 13, 13, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/504 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/504' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 33, 17, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/505 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/505' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 33, 17, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195156718 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 Building ZINC000195156718 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195156718 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 502) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 34, 17, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 13, 13, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 503) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 34, 17, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 13, 13, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 504) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 33, 17, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 505) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 33, 17, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195156718 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 Building ZINC000195156718 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195156718 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 502) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 34, 17, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 13, 13, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 503) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 34, 17, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 13, 13, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 504) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 33, 17, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 505) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 33, 17, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195156718 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 Building ZINC000195156718 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195156718 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 502) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 34, 17, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 13, 13, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 503) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 34, 17, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 13, 13, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 504) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 33, 17, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 505) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156718.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195156718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156718 none C[C@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 33, 17, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195156718 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195156718 Building ZINC000408102338 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408102338 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/506 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@@H]2CCCO2)cn1) `ZINC000408102338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408102338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102338 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 2, 9, 12, 15, 15, 15, 15, 15, 15, 20, 31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 9] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/507 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@@H]2CCCO2)cn1) `ZINC000408102338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408102338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102338 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 12, 12, 14, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408102338 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 Building ZINC000408102338 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408102338 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 506) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@@H]2CCCO2)cn1) `ZINC000408102338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408102338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102338 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 2, 9, 12, 15, 15, 15, 15, 15, 15, 20, 31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 9] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 507) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@@H]2CCCO2)cn1) `ZINC000408102338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408102338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102338 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 12, 12, 14, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408102338 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102338 Building ZINC000408102339 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408102339 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/508 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@H]2CCCO2)cn1) `ZINC000408102339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408102339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102339 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 12, 12, 14, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/509 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@H]2CCCO2)cn1) `ZINC000408102339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408102339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102339 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 2, 9, 12, 14, 14, 14, 14, 14, 14, 19, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 9] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408102339 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 Building ZINC000408102339 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408102339 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 508) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@H]2CCCO2)cn1) `ZINC000408102339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408102339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102339 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 12, 12, 14, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 509) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@H]2CCCO2)cn1) `ZINC000408102339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408102339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102339 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 2, 9, 12, 14, 14, 14, 14, 14, 14, 19, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 9] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408102339 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102339 Building ZINC000408102340 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408102340 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/510 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@@H]2CCCO2)cn1) `ZINC000408102340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408102340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102340 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 12, 12, 14, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/511 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@@H]2CCCO2)cn1) `ZINC000408102340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408102340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102340 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 2, 10, 13, 15, 15, 15, 15, 15, 15, 16, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408102340 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 Building ZINC000408102340 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408102340 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 510) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@@H]2CCCO2)cn1) `ZINC000408102340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408102340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102340 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 12, 12, 14, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 511) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@@H]2CCCO2)cn1) `ZINC000408102340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408102340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102340 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2[C@@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 2, 10, 13, 15, 15, 15, 15, 15, 15, 16, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408102340 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102340 Building ZINC000408102341 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408102341 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/512 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@H]2CCCO2)cn1) `ZINC000408102341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408102341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102341 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 2, 11, 14, 16, 16, 16, 16, 16, 16, 17, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/513 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@H]2CCCO2)cn1) `ZINC000408102341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408102341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102341 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 12, 12, 14, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408102341 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 Building ZINC000408102341 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408102341 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 512) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@H]2CCCO2)cn1) `ZINC000408102341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408102341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102341 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 2, 11, 14, 16, 16, 16, 16, 16, 16, 17, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 513) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@H]2CCCO2)cn1) `ZINC000408102341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408102341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000408102341 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2[C@H]2CCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 7, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 12, 12, 14, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408102341 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408102341 Building ZINC000195176628 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195176628 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/514 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN1CCCC1) `ZINC000195176628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195176628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000195176628 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 30, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 28, 32, 34, 34, 34, 34, 30, 30, 30, 15, 15, 3, 7, 7, 7, 7, 7, 32, 32, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/515 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN1CCCC1) `ZINC000195176628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195176628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000195176628 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 30, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 36, 36, 36, 36, 30, 30, 30, 14, 14, 2, 6, 6, 6, 6, 6, 30, 30, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195176628 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 Building ZINC000195176628 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195176628 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 514) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN1CCCC1) `ZINC000195176628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195176628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000195176628 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 30, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 28, 32, 34, 34, 34, 34, 30, 30, 30, 15, 15, 3, 7, 7, 7, 7, 7, 32, 32, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 515) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN1CCCC1) `ZINC000195176628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195176628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000195176628 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 30, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 36, 36, 36, 36, 30, 30, 30, 14, 14, 2, 6, 6, 6, 6, 6, 30, 30, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195176628 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176628 Building ZINC000195182369 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195182369 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/516 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CCCO1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195182369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195182369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000195182369 none CCN(C[C@H]1CCCO1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 4, 7, 17, 22, 22, 22, 22, 22, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 5, 5, 5, 5, 5] 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]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/517 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CCCO1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195182369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195182369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000195182369 none CCN(C[C@H]1CCCO1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 4, 9, 20, 28, 28, 28, 28, 28, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 15, 15, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195182369 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 Building ZINC000195182369 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195182369 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 516) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN(C[C@H]1CCCO1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195182369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195182369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000195182369 none CCN(C[C@H]1CCCO1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 4, 7, 17, 22, 22, 22, 22, 22, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 5, 5, 5, 5, 5] 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]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 517) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN(C[C@H]1CCCO1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195182369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195182369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000195182369 none CCN(C[C@H]1CCCO1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 4, 9, 20, 28, 28, 28, 28, 28, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 15, 15, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195182369 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195182369 Building ZINC000336146764 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336146764 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/518 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1) `ZINC000336146764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336146764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000336146764 none CC(C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 21, 34, 21, 21, 21, 10, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/519 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1) `ZINC000336146764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336146764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000336146764 none CC(C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 31, 16, 16, 16, 9, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 107 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000336146764 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 Building ZINC000336146764 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336146764 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 518) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1) `ZINC000336146764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336146764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000336146764 none CC(C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 21, 34, 21, 21, 21, 10, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 519) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1) `ZINC000336146764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336146764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000336146764 none CC(C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 31, 16, 16, 16, 9, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 107 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000336146764 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000336146764 Building ZINC000110800503 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110800503 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/520 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn2cc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc12) `ZINC000110800503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110800503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000110800503 none Cc1cccn2cc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [34, 34, 34, 34, 34, 34, 34, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 2, 5, 5, 5, 5, 5] 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: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/521 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn2cc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc12) `ZINC000110800503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110800503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000110800503 none Cc1cccn2cc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [35, 35, 35, 35, 35, 35, 35, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 14, 2, 5, 5, 5, 5, 5] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000110800503 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 Building ZINC000110800503 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110800503 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 520) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1cccn2cc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc12) `ZINC000110800503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110800503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000110800503 none Cc1cccn2cc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [34, 34, 34, 34, 34, 34, 34, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 2, 5, 5, 5, 5, 5] 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: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 521) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1cccn2cc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc12) `ZINC000110800503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110800503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000110800503 none Cc1cccn2cc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [35, 35, 35, 35, 35, 35, 35, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 14, 2, 5, 5, 5, 5, 5] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000110800503 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000110800503 Building ZINC000408106808 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408106808 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/522 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000408106808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408106808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408106808 none COC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 4, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 63 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/523 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000408106808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408106808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408106808 none COC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 6, 1, 8, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 32, 32, 32, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408106808 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 Building ZINC000408106808 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408106808 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 522) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000408106808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408106808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408106808 none COC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 4, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 63 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 523) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000408106808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408106808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408106808 none COC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 6, 1, 8, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 32, 32, 32, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408106808 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408106808 Building ZINC000617030124 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617030124 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/524 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000617030124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617030124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000617030124 none CCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 8, 11, 5, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 22, 22, 22, 22, 22, 11, 8, 8, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/525 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000617030124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617030124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000617030124 none CCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 10, 8, 10, 5, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 18, 18, 18, 18, 18, 10, 8, 8, 5, 5, 5, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000617030124 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 Building ZINC000617030124 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617030124 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 524) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000617030124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617030124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000617030124 none CCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 8, 11, 5, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 22, 22, 22, 22, 22, 11, 8, 8, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 525) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000617030124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617030124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000617030124 none CCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 10, 8, 10, 5, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 18, 18, 18, 18, 18, 10, 8, 8, 5, 5, 5, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000617030124 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000617030124 Building ZINC000106363913 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106363913 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/526 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/526' -> `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])c2cnn(C)c2)C1) `ZINC000106363913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106363913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000106363913 none CN(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 29, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 13, 29, 29, 29, 29, 29, 29, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 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]) total number of confs: 85 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/527 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/527' -> `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])c2cnn(C)c2)C1) `ZINC000106363913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106363913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000106363913 none CN(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 25, 13, 13, 13, 13, 13, 7, 2, 8, 1, 1, 1, 8, 8, 8, 8, 8, 13, 25, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 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]) total number of confs: 77 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106363913 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 Building ZINC000106363913 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106363913 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 526) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000106363913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106363913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000106363913 none CN(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 29, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 13, 29, 29, 29, 29, 29, 29, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 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]) total number of confs: 85 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 527) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000106363913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106363913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000106363913 none CN(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 25, 13, 13, 13, 13, 13, 7, 2, 8, 1, 1, 1, 8, 8, 8, 8, 8, 13, 25, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 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]) total number of confs: 77 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106363913 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363913 Building ZINC000106363914 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106363914 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/528 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/528' -> `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])c2cnn(C)c2)C1) `ZINC000106363914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106363914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000106363914 none CN(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 28, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 7, 7, 7, 7, 7, 16, 28, 28, 28, 28, 28, 28, 16, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 16, 16] 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]) total number of confs: 78 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/529 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/529' -> `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])c2cnn(C)c2)C1) `ZINC000106363914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106363914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000106363914 none CN(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 11, 30, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 11, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 88 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106363914 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 Building ZINC000106363914 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106363914 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 528) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000106363914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106363914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000106363914 none CN(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 28, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 7, 7, 7, 7, 7, 16, 28, 28, 28, 28, 28, 28, 16, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 16, 16] 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]) total number of confs: 78 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 529) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000106363914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106363914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC000106363914 none CN(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 11, 30, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 11, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 88 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000106363914 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000106363914 Building ZINC000909344387 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909344387 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/530 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000909344387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909344387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000909344387 none CCC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 12, 24, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 12, 12, 12, 12, 12, 12, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/531 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000909344387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909344387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000909344387 none CCC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 22, 9, 22, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000909344387 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 Building ZINC000909344387 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909344387 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 530) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000909344387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909344387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000909344387 none CCC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 12, 24, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 12, 12, 12, 12, 12, 12, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 531) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000909344387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909344387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000909344387 none CCC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 22, 9, 22, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000909344387 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000909344387 Building ZINC000840922045 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840922045 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/532 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H](CO)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840922045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840922045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922045 none CS[C@H](CO)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 14, 5, 7, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 32, 13, 32, 29, 35, 4, 13, 13, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 40, 35, 35, 105, 13, 13, 13, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 286 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/533 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H](CO)[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840922045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840922045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922045 none CS[C@H](CO)[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 14, 5, 7, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 33, 11, 33, 28, 39, 3, 11, 11, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 40, 39, 39, 117, 11, 11, 11, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 324 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000840922045 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 Building ZINC000840922045 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840922045 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 532) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H](CO)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840922045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840922045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922045 none CS[C@H](CO)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 14, 5, 7, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 32, 13, 32, 29, 35, 4, 13, 13, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 40, 35, 35, 105, 13, 13, 13, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 286 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 533) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H](CO)[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840922045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840922045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922045 none CS[C@H](CO)[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 14, 5, 7, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 33, 11, 33, 28, 39, 3, 11, 11, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 40, 39, 39, 117, 11, 11, 11, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 324 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000840922045 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922045 Building ZINC000195176806 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195176806 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/534 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)nc2)cn1) `ZINC000195176806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195176806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000195176806 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 2, 14, 14, 33, 33, 33, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/535 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)nc2)cn1) `ZINC000195176806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195176806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000195176806 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 14, 14, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195176806 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 Building ZINC000195176806 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195176806 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 534) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)nc2)cn1) `ZINC000195176806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195176806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000195176806 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 2, 14, 14, 33, 33, 33, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 535) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)nc2)cn1) `ZINC000195176806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195176806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000195176806 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 14, 14, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195176806 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195176806 Building ZINC000195281511 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195281511 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/536 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195281511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195281511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000195281511 none CCOC(=O)CN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 5, 25, 3, 2, 3, 6, 6, 6, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/537 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(CC(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195281511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195281511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000195281511 none CCOC(=O)CN(CC(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 33, 7, 33, 4, 2, 4, 6, 6, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195281511 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 Building ZINC000195281511 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195281511 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 536) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195281511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195281511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000195281511 none CCOC(=O)CN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 5, 25, 3, 2, 3, 6, 6, 6, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 537) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(CC(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195281511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195281511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000195281511 none CCOC(=O)CN(CC(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 33, 7, 33, 4, 2, 4, 6, 6, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000195281511 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000195281511 Building ZINC000408129497 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408129497 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/538 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000408129497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408129497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408129497 none COC1(C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 14, 14, 14, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 21, 21, 21, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14] 39 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]) total number of confs: 38 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/539 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000408129497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408129497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408129497 none COC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 14, 22, 22, 22, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14] 43 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]) total number of confs: 42 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408129497 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 Building ZINC000408129497 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408129497 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 538) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC1(C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000408129497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408129497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408129497 none COC1(C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 14, 14, 14, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 21, 21, 21, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14] 39 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]) total number of confs: 38 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 539) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000408129497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408129497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408129497 none COC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 14, 22, 22, 22, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14] 43 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]) total number of confs: 42 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408129497 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408129497 Building ZINC000408143550 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408143550 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/540 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000408143550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408143550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408143550 none CC(C)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 15, 28, 15, 15, 15, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 15, 15, 6, 6, 6, 6, 6, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/541 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000408143550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408143550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408143550 none CC(C)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 14, 30, 14, 14, 14, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 14, 14, 6, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408143550 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 Building ZINC000408143550 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408143550 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 540) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000408143550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408143550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408143550 none CC(C)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 15, 28, 15, 15, 15, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 15, 15, 6, 6, 6, 6, 6, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 541) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000408143550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408143550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408143550 none CC(C)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 14, 30, 14, 14, 14, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 14, 14, 6, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408143550 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143550 Building ZINC000408143551 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408143551 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/542 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000408143551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408143551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408143551 none CC(C)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 12, 28, 12, 12, 12, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 12, 12, 7, 7, 7, 7, 7, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/543 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000408143551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408143551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408143551 none CC(C)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 29, 15, 15, 15, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 15, 15, 6, 6, 6, 6, 6, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408143551 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 Building ZINC000408143551 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408143551 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 542) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000408143551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408143551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408143551 none CC(C)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 12, 28, 12, 12, 12, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 12, 12, 7, 7, 7, 7, 7, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 543) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000408143551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408143551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000408143551 none CC(C)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 29, 15, 15, 15, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 15, 15, 6, 6, 6, 6, 6, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408143551 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408143551 Building ZINC000840922843 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840922843 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/544 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840922843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840922843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922843 none CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 31, 5, 1, 5, 1, 1, 2, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/545 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840922843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840922843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922843 none CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 31, 4, 1, 4, 1, 1, 2, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 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: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000840922843 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 Building ZINC000840922843 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840922843 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 544) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840922843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840922843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922843 none CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 31, 5, 1, 5, 1, 1, 2, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 545) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840922843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840922843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922843 none CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 31, 4, 1, 4, 1, 1, 2, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 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: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000840922843 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840922843 Building ZINC000957027520 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000957027520 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/546 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(O)(C2CC2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000957027520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000957027520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000957027520 none O=C(N1CC(O)(C2CC2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 8, 26, 26, 26, 26, 46, 46, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 78, 46, 46, 46, 46, 46, 26, 26, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 204 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/547 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(O)(C2CC2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000957027520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000957027520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000957027520 none O=C(N1CC(O)(C2CC2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 8, 24, 24, 24, 24, 48, 48, 24, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 72, 48, 48, 48, 48, 48, 24, 24, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 205 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000957027520 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 Building ZINC000957027520 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000957027520 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 546) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N1CC(O)(C2CC2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000957027520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000957027520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000957027520 none O=C(N1CC(O)(C2CC2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 8, 26, 26, 26, 26, 46, 46, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 78, 46, 46, 46, 46, 46, 26, 26, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 204 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 547) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N1CC(O)(C2CC2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000957027520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000957027520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000957027520 none O=C(N1CC(O)(C2CC2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 8, 24, 24, 24, 24, 48, 48, 24, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 72, 48, 48, 48, 48, 48, 24, 24, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 205 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000957027520 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000957027520 Building ZINC000613768623 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613768623 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/548 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/548' -> `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[nH]n2)cn1) `ZINC000613768623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613768623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000613768623 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cc[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 6, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 13, 13, 22, 22, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/549 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/549' -> `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[nH]n2)cn1) `ZINC000613768623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613768623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000613768623 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cc[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 6, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 13, 13, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613768623 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 Building ZINC000613768623 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613768623 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 548) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cc[nH]n2)cn1) `ZINC000613768623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613768623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000613768623 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cc[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 6, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 13, 13, 22, 22, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 549) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cc[nH]n2)cn1) `ZINC000613768623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613768623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000613768623 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cc[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 6, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 13, 13, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613768623 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613768623 Building ZINC000343873838 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343873838 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/550 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC(C)(C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000343873838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343873838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000343873838 none CCOC(=O)CC(C)(C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 15, 27, 7, 3, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 15, 15, 7, 7, 7, 7, 7, 7, 3, 3, 3, 4, 4, 4, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/551 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC(C)(C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000343873838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343873838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000343873838 none CCOC(=O)CC(C)(C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 27, 6, 3, 6, 6, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 31, 31, 31, 31, 31, 14, 14, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000343873838 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 Building ZINC000343873838 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343873838 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 550) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC(C)(C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000343873838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343873838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000343873838 none CCOC(=O)CC(C)(C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 15, 27, 7, 3, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 15, 15, 7, 7, 7, 7, 7, 7, 3, 3, 3, 4, 4, 4, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 551) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC(C)(C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000343873838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343873838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000343873838 none CCOC(=O)CC(C)(C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 27, 6, 3, 6, 6, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 31, 31, 31, 31, 31, 14, 14, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000343873838 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000343873838 Building ZINC000976003252 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976003252 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/552 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976003252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976003252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000976003252 none CCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 26, 26, 26, 8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 41, 41, 41, 41, 41, 26, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8] 41 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/553 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976003252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976003252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000976003252 none CCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 22, 22, 22, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 39, 39, 39, 39, 39, 22, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 39 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976003252 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 Building ZINC000976003252 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976003252 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 552) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976003252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976003252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000976003252 none CCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 26, 26, 26, 8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 41, 41, 41, 41, 41, 26, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8] 41 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 553) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976003252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976003252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000976003252 none CCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 22, 22, 22, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 39, 39, 39, 39, 39, 22, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 39 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976003252 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976003252 Building ZINC000976008128 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976008128 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/554 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976008128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976008128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000976008128 none CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 3, 10, 10, 10, 25, 25, 25, 25, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10] 25 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]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/555 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976008128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976008128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000976008128 none CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 22, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 22, 22, 22, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10] 23 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]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976008128 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 Building ZINC000976008128 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976008128 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 554) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976008128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976008128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000976008128 none CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 3, 10, 10, 10, 25, 25, 25, 25, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10] 25 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]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 555) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976008128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976008128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000976008128 none CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 22, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 22, 22, 22, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10] 23 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]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976008128 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976008128 Building ZINC000976011097 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976011097 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/556 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(F)F) `ZINC000976011097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976011097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000976011097 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 31, 31, 31, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 31, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/557 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(F)F) `ZINC000976011097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976011097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000976011097 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 30, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 30, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976011097 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 Building ZINC000976011097 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976011097 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 556) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(F)F) `ZINC000976011097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976011097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000976011097 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 31, 31, 31, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 31, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 557) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(F)F) `ZINC000976011097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976011097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000976011097 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 30, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 30, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976011097 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976011097 Building ZINC000976015646 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976015646 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/558 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CC1) `ZINC000976015646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976015646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000976015646 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 23, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/559 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CC1) `ZINC000976015646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976015646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000976015646 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 31, 31, 31, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976015646 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 Building ZINC000976015646 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976015646 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 558) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CC1) `ZINC000976015646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976015646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000976015646 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 23, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 559) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CC1) `ZINC000976015646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976015646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000976015646 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 31, 31, 31, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976015646 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976015646 Building ZINC000976025250 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976025250 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/560 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CCC1) `ZINC000976025250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976025250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976025250 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/561 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CCC1) `ZINC000976025250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976025250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976025250 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976025250 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 Building ZINC000976025250 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976025250 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 560) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CCC1) `ZINC000976025250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976025250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976025250 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 561) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CCC1) `ZINC000976025250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976025250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976025250 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976025250 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976025250 Building ZINC000976033488 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976033488 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/562 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(C)(C)F) `ZINC000976033488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000976033488 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/563 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(C)(C)F) `ZINC000976033488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000976033488 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 25, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976033488 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 Building ZINC000976033488 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976033488 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 562) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(C)(C)F) `ZINC000976033488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000976033488 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 563) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(C)(C)F) `ZINC000976033488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000976033488 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 25, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976033488 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976033488 Building ZINC000976055577 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976055577 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/564 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CC1CC1) `ZINC000976055577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976055577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976055577 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 37, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 37, 37, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/565 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CC1CC1) `ZINC000976055577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976055577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976055577 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 38, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976055577 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 Building ZINC000976055577 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976055577 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 564) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CC1CC1) `ZINC000976055577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976055577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976055577 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 37, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 37, 37, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 565) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CC1CC1) `ZINC000976055577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976055577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976055577 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 38, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976055577 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976055577 Building ZINC000976103557 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976103557 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/566 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976103557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103557 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 23, 23, 7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/567 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976103557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103557 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 50, 20, 20, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 20, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976103557 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 Building ZINC000976103557 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976103557 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 566) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976103557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103557 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 23, 23, 7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 567) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976103557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103557 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 50, 20, 20, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 20, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976103557 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103557 Building ZINC000976103561 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976103561 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/568 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976103561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103561 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 50, 21, 21, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/569 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976103561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103561 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 50, 19, 19, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976103561 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 Building ZINC000976103561 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976103561 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 568) grep: /scratch/xiaobo/170854/xdl-8058088.90/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[C@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976103561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103561 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 50, 21, 21, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 569) grep: /scratch/xiaobo/170854/xdl-8058088.90/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[C@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976103561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103561 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 50, 19, 19, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976103561 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103561 Building ZINC000976103565 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976103565 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/570 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976103565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103565 none C[C@@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 28, 28, 7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/571 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976103565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103565 none C[C@@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 50, 31, 31, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976103565 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 Building ZINC000976103565 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976103565 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 570) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976103565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103565 none C[C@@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 28, 28, 7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 571) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976103565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103565 none C[C@@H]1C[C@@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 50, 31, 31, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976103565 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103565 Building ZINC000976103568 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976103568 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/572 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976103568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103568 none C[C@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 29, 29, 7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/573 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976103568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103568 none C[C@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 50, 27, 27, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976103568 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 Building ZINC000976103568 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976103568 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 572) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976103568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103568 none C[C@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 29, 29, 7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 573) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976103568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976103568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976103568 none C[C@H]1C[C@H]1C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 50, 27, 27, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976103568 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976103568 Building ZINC000976191524 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976191524 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/574 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976191524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976191524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000976191524 none CC(C)C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 40, 34, 34, 8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 40, 40, 40, 40, 40, 40, 40, 34, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8] 40 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/575 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976191524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976191524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000976191524 none CC(C)C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 35, 38, 35, 35, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 38, 38, 38, 38, 38, 38, 38, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 38 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976191524 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 Building ZINC000976191524 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976191524 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 574) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976191524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976191524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000976191524 none CC(C)C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 40, 34, 34, 8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 40, 40, 40, 40, 40, 40, 40, 34, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8] 40 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 575) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000976191524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976191524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000976191524 none CC(C)C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 35, 38, 35, 35, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 38, 38, 38, 38, 38, 38, 38, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 38 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976191524 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976191524 Building ZINC001027337600 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001027337600 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/576 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 13, 40, 50, 50, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 150, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 309 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/577 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 39, 50, 50, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 39, 39, 39, 50, 50, 50, 50, 150, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 308 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/578 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/578' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 13, 40, 50, 50, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 150, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 309 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/579 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/579' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 39, 50, 50, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 39, 39, 39, 50, 50, 50, 50, 150, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 308 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001027337600 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 Building ZINC001027337600 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001027337600 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 576) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 13, 40, 50, 50, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 150, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 309 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 577) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 39, 50, 50, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 39, 39, 39, 50, 50, 50, 50, 150, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 308 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 578) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 13, 40, 50, 50, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 150, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 309 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 579) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 39, 50, 50, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 39, 39, 39, 50, 50, 50, 50, 150, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 308 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001027337600 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 Building ZINC001027337600 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001027337600 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 576) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 13, 40, 50, 50, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 150, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 309 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 577) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 39, 50, 50, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 39, 39, 39, 50, 50, 50, 50, 150, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 308 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 578) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 13, 40, 50, 50, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 150, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 309 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 579) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 39, 50, 50, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 39, 39, 39, 50, 50, 50, 50, 150, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 308 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001027337600 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 Building ZINC001027337600 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001027337600 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 576) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 13, 40, 50, 50, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 150, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 309 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 577) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 39, 50, 50, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 39, 39, 39, 50, 50, 50, 50, 150, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 308 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 578) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 13, 40, 50, 50, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 150, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 309 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 579) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027337600.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001027337600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001027337600 none CN(CCO)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 39, 50, 50, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 39, 39, 39, 50, 50, 50, 50, 150, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 308 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001027337600 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027337600 Building ZINC001027338123 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001027338123 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/580 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 50, 50, 11, 29, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 50, 50, 29, 29, 29, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/581 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 50, 50, 11, 29, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 50, 50, 29, 29, 29, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/582 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/582' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 45, 45, 50, 50, 16, 34, 16, 16, 16, 16, 16, 13, 1, 13, 1, 1, 1, 1, 1, 1, 16, 45, 45, 45, 50, 50, 34, 34, 34, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/583 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/583' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 45, 45, 50, 50, 16, 34, 16, 16, 16, 16, 16, 13, 1, 13, 1, 1, 1, 1, 1, 1, 16, 45, 45, 45, 50, 50, 34, 34, 34, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001027338123 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 Building ZINC001027338123 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001027338123 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 580) grep: /scratch/xiaobo/170854/xdl-8058088.90/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](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 50, 50, 11, 29, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 50, 50, 29, 29, 29, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 581) grep: /scratch/xiaobo/170854/xdl-8058088.90/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](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 50, 50, 11, 29, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 50, 50, 29, 29, 29, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 582) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 45, 45, 50, 50, 16, 34, 16, 16, 16, 16, 16, 13, 1, 13, 1, 1, 1, 1, 1, 1, 16, 45, 45, 45, 50, 50, 34, 34, 34, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 583) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 45, 45, 50, 50, 16, 34, 16, 16, 16, 16, 16, 13, 1, 13, 1, 1, 1, 1, 1, 1, 16, 45, 45, 45, 50, 50, 34, 34, 34, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001027338123 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 Building ZINC001027338123 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001027338123 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 580) grep: /scratch/xiaobo/170854/xdl-8058088.90/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](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 50, 50, 11, 29, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 50, 50, 29, 29, 29, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 581) grep: /scratch/xiaobo/170854/xdl-8058088.90/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](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 50, 50, 11, 29, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 50, 50, 29, 29, 29, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 582) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 45, 45, 50, 50, 16, 34, 16, 16, 16, 16, 16, 13, 1, 13, 1, 1, 1, 1, 1, 1, 16, 45, 45, 45, 50, 50, 34, 34, 34, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 583) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 45, 45, 50, 50, 16, 34, 16, 16, 16, 16, 16, 13, 1, 13, 1, 1, 1, 1, 1, 1, 16, 45, 45, 45, 50, 50, 34, 34, 34, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001027338123 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 Building ZINC001027338123 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001027338123 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 580) grep: /scratch/xiaobo/170854/xdl-8058088.90/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](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 50, 50, 11, 29, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 50, 50, 29, 29, 29, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 581) grep: /scratch/xiaobo/170854/xdl-8058088.90/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](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 50, 50, 11, 29, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 50, 50, 29, 29, 29, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 582) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 45, 45, 50, 50, 16, 34, 16, 16, 16, 16, 16, 13, 1, 13, 1, 1, 1, 1, 1, 1, 16, 45, 45, 45, 50, 50, 34, 34, 34, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 583) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001027338123.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001027338123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001027338123 none C[C@H](C(N)=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 11, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 45, 45, 50, 50, 16, 34, 16, 16, 16, 16, 16, 13, 1, 13, 1, 1, 1, 1, 1, 1, 16, 45, 45, 45, 50, 50, 34, 34, 34, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001027338123 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001027338123 Building ZINC000408167980 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408167980 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/584 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)[C@@H](C)C2)cn1) `ZINC000408167980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408167980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408167980 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 6, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 16, 16, 16, 16, 16, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/585 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)[C@@H](C)C2)cn1) `ZINC000408167980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408167980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408167980 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 6, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 16, 16, 16, 16, 16, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408167980 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 Building ZINC000408167980 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408167980 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 584) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)[C@@H](C)C2)cn1) `ZINC000408167980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408167980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408167980 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 6, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 16, 16, 16, 16, 16, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 585) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)[C@@H](C)C2)cn1) `ZINC000408167980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408167980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408167980 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 6, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 16, 16, 16, 16, 16, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408167980 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408167980 Building ZINC000976643261 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976643261 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/586 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1(C)CC1) `ZINC000976643261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976643261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976643261 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 25, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/587 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1(C)CC1) `ZINC000976643261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976643261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976643261 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 23, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976643261 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 Building ZINC000976643261 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000976643261 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 586) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1(C)CC1) `ZINC000976643261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000976643261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976643261 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 25, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 587) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1(C)CC1) `ZINC000976643261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000976643261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000976643261 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 23, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000976643261 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000976643261 Building ZINC000408176266 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408176266 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/588 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](O)CC1) `ZINC000408176266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408176266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408176266 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 26, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 120, 40, 40, 40, 40] 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]) total number of confs: 186 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/589 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](O)CC1) `ZINC000408176266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408176266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408176266 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 11, 23, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 39, 39, 39, 39, 39, 39, 117, 39, 39, 39, 39] 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]) total number of confs: 179 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408176266 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 Building ZINC000408176266 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408176266 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 588) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](O)CC1) `ZINC000408176266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408176266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408176266 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 26, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 120, 40, 40, 40, 40] 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]) total number of confs: 186 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 589) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](O)CC1) `ZINC000408176266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408176266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408176266 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 11, 23, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 39, 39, 39, 39, 39, 39, 117, 39, 39, 39, 39] 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]) total number of confs: 179 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408176266 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176266 Building ZINC000408176269 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408176269 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/590 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](O)CC1) `ZINC000408176269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408176269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408176269 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 19, 27, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 120, 40, 40, 40, 40] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 196 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/591 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](O)CC1) `ZINC000408176269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408176269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408176269 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 20, 27, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 41, 41, 41, 41, 41, 41, 123, 41, 41, 41, 41] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408176269 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 Building ZINC000408176269 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408176269 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 590) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](O)CC1) `ZINC000408176269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408176269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408176269 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 19, 27, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 120, 40, 40, 40, 40] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 196 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 591) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](O)CC1) `ZINC000408176269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408176269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408176269 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 20, 27, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 41, 41, 41, 41, 41, 41, 123, 41, 41, 41, 41] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408176269 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176269 Building ZINC000408176840 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408176840 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/592 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)CC2)cn1) `ZINC000408176840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408176840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408176840 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 5, 10, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 16, 16, 16, 16, 16, 5, 17, 17, 17, 17, 17, 17, 51, 17, 17, 17, 17, 5] 150 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/593 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)CC2)cn1) `ZINC000408176840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408176840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408176840 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 6, 9, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 14, 14, 14, 14, 14, 4, 15, 15, 15, 15, 15, 15, 45, 15, 15, 15, 15, 4] 150 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408176840 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 Building ZINC000408176840 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408176840 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 592) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)CC2)cn1) `ZINC000408176840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408176840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408176840 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 5, 10, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 16, 16, 16, 16, 16, 5, 17, 17, 17, 17, 17, 17, 51, 17, 17, 17, 17, 5] 150 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 593) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)CC2)cn1) `ZINC000408176840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408176840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408176840 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 6, 9, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 14, 14, 14, 14, 14, 4, 15, 15, 15, 15, 15, 15, 45, 15, 15, 15, 15, 4] 150 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408176840 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176840 Building ZINC000408176842 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408176842 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/594 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](O)CC2)cn1) `ZINC000408176842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408176842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408176842 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 5, 5, 1, 1, 1, 2, 7, 10, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 15, 15, 15, 15, 15, 5, 15, 15, 15, 15, 15, 15, 45, 15, 15, 15, 15, 5] 150 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/595 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](O)CC2)cn1) `ZINC000408176842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408176842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408176842 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 4, 4, 1, 1, 1, 2, 8, 11, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 15, 15, 15, 15, 15, 4, 14, 14, 14, 14, 14, 14, 42, 14, 14, 14, 14, 4] 150 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408176842 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 Building ZINC000408176842 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408176842 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 594) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](O)CC2)cn1) `ZINC000408176842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408176842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408176842 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 5, 5, 1, 1, 1, 2, 7, 10, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 15, 15, 15, 15, 15, 5, 15, 15, 15, 15, 15, 15, 45, 15, 15, 15, 15, 5] 150 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 595) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](O)CC2)cn1) `ZINC000408176842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408176842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000408176842 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 4, 4, 1, 1, 1, 2, 8, 11, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 15, 15, 15, 15, 15, 4, 14, 14, 14, 14, 14, 14, 42, 14, 14, 14, 14, 4] 150 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408176842 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408176842 Building ZINC000408182717 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408182717 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/596 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/596' -> `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@]1(C)CCO[C@@H]1C) `ZINC000408182717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408182717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182717 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 14, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 22 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/597 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/597' -> `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@]1(C)CCO[C@@H]1C) `ZINC000408182717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408182717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182717 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 10, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 15 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 40 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408182717 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 Building ZINC000408182717 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408182717 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 596) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@@H]1C) `ZINC000408182717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408182717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182717 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 14, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 22 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 597) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@@H]1C) `ZINC000408182717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408182717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182717 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 10, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 15 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 40 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408182717 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182717 Building ZINC000408182719 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408182719 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/598 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/598' -> `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@@]1(C)CCO[C@@H]1C) `ZINC000408182719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408182719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182719 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 26 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/599 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/599' -> `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@@]1(C)CCO[C@@H]1C) `ZINC000408182719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408182719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182719 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 12, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 74 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408182719 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 Building ZINC000408182719 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408182719 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 598) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@@H]1C) `ZINC000408182719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408182719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182719 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 26 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 599) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@@H]1C) `ZINC000408182719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408182719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182719 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 12, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 74 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408182719 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182719 Building ZINC000613808999 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613808999 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/600 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000613808999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613808999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613808999 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 23, 23, 23, 23, 12, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 23, 23, 23, 36, 36, 36, 23, 23, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23] 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]) total number of confs: 70 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/601 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000613808999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613808999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613808999 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 22, 22, 22, 22, 13, 1, 13, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 38, 38, 38, 22, 22, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22] 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]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613808999 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 Building ZINC000613808999 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613808999 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 600) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000613808999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613808999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613808999 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 23, 23, 23, 23, 12, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 23, 23, 23, 36, 36, 36, 23, 23, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23] 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]) total number of confs: 70 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 601) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000613808999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613808999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613808999 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 22, 22, 22, 22, 13, 1, 13, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 38, 38, 38, 22, 22, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22] 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]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613808999 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613808999 Building ZINC000613809003 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613809003 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/602 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000613809003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613809003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613809003 none CO[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 26, 26, 26, 26, 15, 2, 15, 1, 1, 1, 7, 7, 7, 7, 7, 26, 26, 26, 38, 38, 38, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26] 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]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/603 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000613809003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613809003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613809003 none CO[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 24, 24, 24, 24, 13, 2, 13, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 38, 38, 38, 24, 24, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24] 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]) total number of confs: 76 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613809003 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 Building ZINC000613809003 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613809003 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 602) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CO[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000613809003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613809003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613809003 none CO[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 26, 26, 26, 26, 15, 2, 15, 1, 1, 1, 7, 7, 7, 7, 7, 26, 26, 26, 38, 38, 38, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26] 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]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 603) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CO[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000613809003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613809003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613809003 none CO[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 24, 24, 24, 24, 13, 2, 13, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 38, 38, 38, 24, 24, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24] 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]) total number of confs: 76 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613809003 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613809003 Building ZINC000613810658 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613810658 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/604 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000613810658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613810658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613810658 none CO[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 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: [47, 33, 33, 33, 33, 21, 2, 21, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 47, 47, 47, 33, 33, 5, 5, 10, 5, 5, 33, 33, 33, 33] 100 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]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/605 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000613810658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613810658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613810658 none CO[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 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, 33, 33, 33, 33, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 50, 50, 50, 33, 33, 3, 3, 6, 3, 3, 33, 33, 33, 33] 100 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]) total number of confs: 107 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613810658 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 Building ZINC000613810658 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613810658 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 604) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CO[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000613810658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613810658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613810658 none CO[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 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: [47, 33, 33, 33, 33, 21, 2, 21, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 47, 47, 47, 33, 33, 5, 5, 10, 5, 5, 33, 33, 33, 33] 100 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]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 605) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CO[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000613810658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613810658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613810658 none CO[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 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, 33, 33, 33, 33, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 50, 50, 50, 33, 33, 3, 3, 6, 3, 3, 33, 33, 33, 33] 100 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]) total number of confs: 107 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613810658 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810658 Building ZINC000613810668 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613810668 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/606 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000613810668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613810668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613810668 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 35, 35, 35, 35, 21, 1, 21, 1, 1, 1, 4, 4, 1, 1, 4, 4, 35, 35, 35, 49, 49, 49, 35, 35, 4, 4, 8, 4, 4, 35, 35, 35, 35] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/607 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000613810668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613810668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613810668 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 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: [46, 35, 35, 35, 35, 19, 1, 19, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 46, 46, 46, 35, 35, 5, 5, 10, 5, 5, 35, 35, 35, 35] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613810668 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 Building ZINC000613810668 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613810668 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 606) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000613810668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613810668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613810668 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 35, 35, 35, 35, 21, 1, 21, 1, 1, 1, 4, 4, 1, 1, 4, 4, 35, 35, 35, 49, 49, 49, 35, 35, 4, 4, 8, 4, 4, 35, 35, 35, 35] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 607) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000613810668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613810668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000613810668 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 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: [46, 35, 35, 35, 35, 19, 1, 19, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 46, 46, 46, 35, 35, 5, 5, 10, 5, 5, 35, 35, 35, 35] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613810668 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613810668 Building ZINC000408182713 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408182713 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/608 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/608' -> `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@@]1(C)CCO[C@H]1C) `ZINC000408182713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408182713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182713 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 11, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 18 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/609 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/609' -> `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@@]1(C)CCO[C@H]1C) `ZINC000408182713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408182713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182713 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 12, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 20 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 45 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408182713 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 Building ZINC000408182713 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408182713 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 608) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@H]1C) `ZINC000408182713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408182713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182713 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 11, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 18 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 609) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@H]1C) `ZINC000408182713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408182713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182713 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 12, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 20 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 45 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408182713 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182713 Building ZINC000408182715 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408182715 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/610 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/610' -> `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@]1(C)CCO[C@H]1C) `ZINC000408182715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408182715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182715 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 11, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 27 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/611 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/611' -> `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@]1(C)CCO[C@H]1C) `ZINC000408182715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408182715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182715 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 13, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 31 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408182715 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 Building ZINC000408182715 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408182715 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 610) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@H]1C) `ZINC000408182715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408182715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182715 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 11, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 27 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 611) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@H]1C) `ZINC000408182715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408182715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000408182715 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 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, 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] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 13, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 31 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408182715 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408182715 Building ZINC001692392097 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001692392097 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/612 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 19, 19, 19, 19, 35, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 35, 35, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/613 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 18, 20, 20, 20, 20, 34, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 34, 34, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/614 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/614' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 19, 19, 19, 19, 35, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 35, 35, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/615 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/615' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 18, 20, 20, 20, 20, 34, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 34, 34, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001692392097 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 Building ZINC001692392097 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001692392097 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 612) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 19, 19, 19, 19, 35, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 35, 35, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 613) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 18, 20, 20, 20, 20, 34, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 34, 34, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 614) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 19, 19, 19, 19, 35, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 35, 35, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 615) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 18, 20, 20, 20, 20, 34, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 34, 34, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001692392097 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 Building ZINC001692392097 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001692392097 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 612) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 19, 19, 19, 19, 35, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 35, 35, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 613) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 18, 20, 20, 20, 20, 34, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 34, 34, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 614) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 19, 19, 19, 19, 35, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 35, 35, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 615) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 18, 20, 20, 20, 20, 34, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 34, 34, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001692392097 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 Building ZINC001692392097 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001692392097 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 612) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 19, 19, 19, 19, 35, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 35, 35, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 613) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 18, 20, 20, 20, 20, 34, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 34, 34, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 614) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 19, 19, 19, 19, 35, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 35, 35, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 615) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1) `ZINC001692392097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001692392097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001692392097 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccon2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 18, 20, 20, 20, 20, 34, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 34, 34, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001692392097 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001692392097 Building ZINC000613814824 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613814824 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/616 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](OC)C1) `ZINC000613814824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613814824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000613814824 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 12, 5, 5, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 2, 12, 15, 27, 27, 27, 27, 27, 27, 41, 27, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 41, 41, 41, 27, 27] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/617 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](OC)C1) `ZINC000613814824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613814824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000613814824 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 12, 5, 5, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 12, 20, 20, 20, 20, 20, 20, 39, 20, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 39, 39, 39, 20, 20] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613814824 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 Building ZINC000613814824 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613814824 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 616) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](OC)C1) `ZINC000613814824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613814824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000613814824 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 12, 5, 5, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 2, 12, 15, 27, 27, 27, 27, 27, 27, 41, 27, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 41, 41, 41, 27, 27] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 617) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](OC)C1) `ZINC000613814824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613814824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000613814824 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 12, 5, 5, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 12, 20, 20, 20, 20, 20, 20, 39, 20, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 39, 39, 39, 20, 20] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613814824 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814824 Building ZINC000613814825 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613814825 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/618 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](OC)C1) `ZINC000613814825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613814825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000613814825 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 12, 5, 5, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 12, 12, 21, 21, 21, 21, 21, 21, 39, 21, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 39, 39, 39, 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]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/619 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](OC)C1) `ZINC000613814825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613814825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000613814825 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 12, 5, 5, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 15, 15, 26, 26, 26, 26, 26, 26, 40, 26, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 40, 40, 40, 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]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613814825 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 Building ZINC000613814825 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613814825 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 618) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](OC)C1) `ZINC000613814825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613814825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000613814825 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 12, 5, 5, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 12, 12, 21, 21, 21, 21, 21, 21, 39, 21, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 39, 39, 39, 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]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 619) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](OC)C1) `ZINC000613814825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613814825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000613814825 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 12, 5, 5, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 15, 15, 26, 26, 26, 26, 26, 26, 40, 26, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 40, 40, 40, 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]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000613814825 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000613814825 Building ZINC000408187211 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408187211 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/620 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](O)[C@@H]2C1) `ZINC000408187211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408187211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408187211 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](O)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 90, 30, 30] 123 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 138 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/621 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](O)[C@@H]2C1) `ZINC000408187211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408187211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408187211 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](O)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 90, 30, 30] 117 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 138 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408187211 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 Building ZINC000408187211 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408187211 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 620) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](O)[C@@H]2C1) `ZINC000408187211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408187211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408187211 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](O)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 90, 30, 30] 123 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 138 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 621) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](O)[C@@H]2C1) `ZINC000408187211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408187211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000408187211 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CC[C@H](O)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 90, 30, 30] 117 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 138 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408187211 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408187211 Building ZINC000977247299 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000977247299 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/622 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)C[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000977247299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000977247299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000977247299 none CC(=O)N(C)C[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 26, 46, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 46, 46, 46, 26, 26, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 175 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/623 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)C[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000977247299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000977247299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000977247299 none CC(=O)N(C)C[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 30, 47, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 47, 47, 47, 30, 30, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 178 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000977247299 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 Building ZINC000977247299 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000977247299 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 622) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N(C)C[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000977247299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000977247299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000977247299 none CC(=O)N(C)C[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 26, 46, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 46, 46, 46, 26, 26, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 175 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 623) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N(C)C[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000977247299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000977247299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000977247299 none CC(=O)N(C)C[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 30, 47, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 47, 47, 47, 30, 30, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 178 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000977247299 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247299 Building ZINC000977247301 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000977247301 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/624 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)C[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000977247301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000977247301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000977247301 none CC(=O)N(C)C[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 50, 30, 45, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 45, 45, 45, 30, 30, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 178 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/625 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)C[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000977247301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000977247301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000977247301 none CC(=O)N(C)C[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 26, 46, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 46, 46, 46, 26, 26, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 175 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000977247301 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 Building ZINC000977247301 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000977247301 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 624) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N(C)C[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000977247301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000977247301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000977247301 none CC(=O)N(C)C[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 50, 30, 45, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 45, 45, 45, 30, 30, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 178 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 625) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N(C)C[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000977247301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000977247301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000977247301 none CC(=O)N(C)C[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 26, 46, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 46, 46, 46, 26, 26, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 175 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000977247301 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000977247301 Building ZINC000662960835 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000662960835 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/626 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000662960835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000662960835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000662960835 none CNC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 21, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 9, 17, 17, 9, 24, 24, 24, 24, 21, 21, 12, 12, 12, 4, 9, 17, 17, 9, 17, 17, 9] 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/627 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000662960835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000662960835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000662960835 none CNC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 13, 4, 13, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 27, 27, 27, 27, 26, 26, 13, 13, 13, 4, 8, 13, 13, 8, 13, 13, 8] 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000662960835 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 Building ZINC000662960835 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000662960835 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 626) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CNC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000662960835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000662960835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000662960835 none CNC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 21, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 9, 17, 17, 9, 24, 24, 24, 24, 21, 21, 12, 12, 12, 4, 9, 17, 17, 9, 17, 17, 9] 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 627) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CNC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000662960835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000662960835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000662960835 none CNC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 13, 4, 13, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 27, 27, 27, 27, 26, 26, 13, 13, 13, 4, 8, 13, 13, 8, 13, 13, 8] 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000662960835 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960835 Building ZINC000662960839 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000662960839 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/628 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000662960839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000662960839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000662960839 none CNC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 25, 13, 4, 13, 13, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 27, 27, 27, 27, 25, 25, 13, 13, 13, 4, 9, 16, 16, 9, 16, 16, 9] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/629 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000662960839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000662960839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000662960839 none CNC[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 22, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 14, 14, 9, 14, 14, 9, 24, 24, 24, 24, 22, 22, 12, 12, 12, 4, 9, 14, 14, 9, 14, 14, 9] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000662960839 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 Building ZINC000662960839 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000662960839 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 628) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CNC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000662960839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000662960839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000662960839 none CNC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 25, 13, 4, 13, 13, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 27, 27, 27, 27, 25, 25, 13, 13, 13, 4, 9, 16, 16, 9, 16, 16, 9] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 629) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CNC[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000662960839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000662960839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000662960839 none CNC[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 22, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 14, 14, 9, 14, 14, 9, 24, 24, 24, 24, 22, 22, 12, 12, 12, 4, 9, 14, 14, 9, 14, 14, 9] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000662960839 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960839 Building ZINC000662960888 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000662960888 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/630 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000662960888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000662960888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000662960888 none CNC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 14, 14, 14, 14, 13, 13, 8, 8, 8, 3, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/631 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000662960888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000662960888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000662960888 none CNC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 10, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 16, 16, 16, 16, 14, 14, 10, 10, 10, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000662960888 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 Building ZINC000662960888 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000662960888 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 630) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CNC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000662960888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000662960888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000662960888 none CNC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 14, 14, 14, 14, 13, 13, 8, 8, 8, 3, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 631) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CNC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000662960888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000662960888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000662960888 none CNC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 10, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 16, 16, 16, 16, 14, 14, 10, 10, 10, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000662960888 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960888 Building ZINC000662960890 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000662960890 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/632 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000662960890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000662960890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000662960890 none CNC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 10, 4, 10, 10, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 19, 19, 19, 19, 17, 17, 10, 10, 10, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/633 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000662960890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000662960890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000662960890 none CNC[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 9, 3, 9, 9, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 7, 18, 18, 18, 18, 17, 17, 9, 9, 9, 3, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000662960890 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 Building ZINC000662960890 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000662960890 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 632) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CNC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000662960890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000662960890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000662960890 none CNC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 10, 4, 10, 10, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 19, 19, 19, 19, 17, 17, 10, 10, 10, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 633) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CNC[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000662960890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000662960890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000662960890 none CNC[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 9, 3, 9, 9, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 7, 18, 18, 18, 18, 17, 17, 9, 9, 9, 3, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000662960890 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000662960890 Building ZINC000840924339 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840924339 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/634 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840924339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840924339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000840924339 none C[C@@H](O)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 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, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 27, 34, 34, 12, 4, 12, 12, 4, 1, 4, 1, 1, 2, 6, 6, 6, 6, 6, 34, 34, 34, 102, 30, 30, 12, 12, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 13, 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: 268 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/635 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840924339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840924339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000840924339 none C[C@@H](O)C[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 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, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 30, 37, 37, 16, 4, 16, 16, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 37, 111, 32, 32, 16, 16, 16, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 290 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000840924339 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 Building ZINC000840924339 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840924339 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 634) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840924339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840924339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000840924339 none C[C@@H](O)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 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, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 27, 34, 34, 12, 4, 12, 12, 4, 1, 4, 1, 1, 2, 6, 6, 6, 6, 6, 34, 34, 34, 102, 30, 30, 12, 12, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 13, 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: 268 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 635) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840924339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840924339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000840924339 none C[C@@H](O)C[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 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, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 30, 37, 37, 16, 4, 16, 16, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 37, 111, 32, 32, 16, 16, 16, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 290 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000840924339 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840924339 Building ZINC000408189741 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408189741 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/636 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CC[C@H](O)[C@@H]3C2)cn1) `ZINC000408189741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408189741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408189741 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CC[C@H](O)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 5, 5, 1, 1, 1, 1, 3, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 22, 22, 22, 22, 22, 5, 15, 15, 15, 15, 15, 15, 45, 15, 15, 5] 150 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/637 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CC[C@H](O)[C@@H]3C2)cn1) `ZINC000408189741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408189741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408189741 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CC[C@H](O)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 5, 5, 1, 1, 1, 1, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 21, 21, 21, 21, 21, 5, 15, 15, 15, 15, 15, 15, 45, 15, 15, 5] 150 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408189741 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 Building ZINC000408189741 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408189741 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 636) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CC[C@H](O)[C@@H]3C2)cn1) `ZINC000408189741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408189741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408189741 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CC[C@H](O)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 5, 5, 1, 1, 1, 1, 3, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 22, 22, 22, 22, 22, 5, 15, 15, 15, 15, 15, 15, 45, 15, 15, 5] 150 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 637) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CC[C@H](O)[C@@H]3C2)cn1) `ZINC000408189741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408189741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408189741 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CC[C@H](O)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 5, 5, 1, 1, 1, 1, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 21, 21, 21, 21, 21, 5, 15, 15, 15, 15, 15, 15, 45, 15, 15, 5] 150 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408189741 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408189741 Building ZINC000893514613 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000893514613 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/638 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC000893514613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000893514613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000893514613 none CC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 32, 17, 17, 17, 17, 17, 4, 1, 8, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 32, 32, 32, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17] 34 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]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/639 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC000893514613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000893514613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000893514613 none CC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [31, 16, 31, 16, 16, 16, 16, 16, 4, 1, 8, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 31, 31, 31, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16] 33 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]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000893514613 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 Building ZINC000893514613 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000893514613 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 638) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC000893514613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000893514613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000893514613 none CC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 32, 17, 17, 17, 17, 17, 4, 1, 8, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 32, 32, 32, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17] 34 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]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 639) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC000893514613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000893514613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000893514613 none CC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [31, 16, 31, 16, 16, 16, 16, 16, 4, 1, 8, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 31, 31, 31, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16] 33 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]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000893514613 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000893514613 Building ZINC000663011123 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663011123 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/640 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CCNC2)cn1) `ZINC000663011123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663011123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000663011123 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CCNC2)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', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 11, 21, 21, 11, 11, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/641 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CCNC2)cn1) `ZINC000663011123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663011123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000663011123 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CCNC2)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', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 15, 15, 8, 8, 1, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 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/170854/xdl-8058088.90/working/building/ZINC000663011123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663011123 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123 Building ZINC000663011123 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663011123 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 640) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CCNC2)cn1) `ZINC000663011123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663011123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000663011123 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(C)CCNC2)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', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 11, 21, 21, 11, 11, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 641) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CCNC2)cn1) `ZINC000663011123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663011123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000663011123 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C)CCNC2)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', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 15, 15, 8, 8, 1, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 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/170854/xdl-8058088.90/working/building/ZINC000663011123 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663011123 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011123 Building ZINC000663011125 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663011125 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/642 `/scratch/xiaobo/170854/xdl-8058088.90/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)N[C@]2(C)CCNC2)cn1) `ZINC000663011125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663011125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000663011125 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@]2(C)CCNC2)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', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 10, 10, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10] 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/643 `/scratch/xiaobo/170854/xdl-8058088.90/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)N[C@]2(C)CCNC2)cn1) `ZINC000663011125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663011125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000663011125 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(C)CCNC2)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', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 14, 8, 8, 1, 1, 1, 1, 4, 4, 7, 13, 13, 13, 13, 13, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663011125 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 Building ZINC000663011125 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663011125 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 642) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)N[C@]2(C)CCNC2)cn1) `ZINC000663011125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663011125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000663011125 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@]2(C)CCNC2)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', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 10, 10, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10] 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 643) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)N[C@]2(C)CCNC2)cn1) `ZINC000663011125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663011125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000663011125 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(C)CCNC2)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', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 14, 8, 8, 1, 1, 1, 1, 4, 4, 7, 13, 13, 13, 13, 13, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663011125 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663011125 Building ZINC000663010167 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663010167 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/644 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1) `ZINC000663010167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663010167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000663010167 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 20, 20, 20, 20, 20, 20, 20, 4, 11, 16, 16, 11, 16, 16, 11, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/645 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1) `ZINC000663010167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663010167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000663010167 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 17, 17, 11, 17, 17, 11, 17, 17, 17, 17, 17, 17, 17, 5, 11, 17, 17, 17, 17, 17, 11, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663010167 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 Building ZINC000663010167 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663010167 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 644) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1) `ZINC000663010167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663010167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000663010167 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 20, 20, 20, 20, 20, 20, 20, 4, 11, 16, 16, 11, 16, 16, 11, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 645) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1) `ZINC000663010167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663010167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000663010167 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 17, 17, 11, 17, 17, 11, 17, 17, 17, 17, 17, 17, 17, 5, 11, 17, 17, 17, 17, 17, 11, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663010167 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010167 Building ZINC000663010169 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663010169 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/646 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1) `ZINC000663010169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663010169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000663010169 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 20, 20, 20, 20, 20, 20, 20, 4, 10, 13, 13, 10, 13, 13, 10, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/647 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1) `ZINC000663010169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663010169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000663010169 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 15, 15, 11, 15, 15, 11, 17, 17, 17, 17, 17, 17, 17, 4, 11, 15, 15, 15, 15, 15, 11, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663010169 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 Building ZINC000663010169 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663010169 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 646) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1) `ZINC000663010169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663010169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000663010169 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 20, 20, 20, 20, 20, 20, 20, 4, 10, 13, 13, 10, 13, 13, 10, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 647) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1) `ZINC000663010169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663010169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000663010169 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CCNC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 15, 15, 11, 15, 15, 11, 17, 17, 17, 17, 17, 17, 17, 4, 11, 15, 15, 15, 15, 15, 11, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663010169 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663010169 Building ZINC000119501366 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119501366 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/648 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)cn1) `ZINC000119501366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119501366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000119501366 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)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', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 14, 15, 15, 15, 15, 15, 7, 7, 21, 21, 21, 21, 21, 7, 3, 14, 14, 45, 15, 15, 15, 15, 15, 15, 7] 150 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/649 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)cn1) `ZINC000119501366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119501366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000119501366 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)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', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 14, 15, 15, 15, 15, 15, 7, 7, 20, 20, 20, 20, 20, 7, 3, 14, 14, 45, 15, 15, 15, 15, 15, 15, 7] 150 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000119501366 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 Building ZINC000119501366 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119501366 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 648) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)cn1) `ZINC000119501366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119501366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000119501366 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)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', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 14, 15, 15, 15, 15, 15, 7, 7, 21, 21, 21, 21, 21, 7, 3, 14, 14, 45, 15, 15, 15, 15, 15, 15, 7] 150 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 649) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)cn1) `ZINC000119501366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119501366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000119501366 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)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', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 14, 15, 15, 15, 15, 15, 7, 7, 20, 20, 20, 20, 20, 7, 3, 14, 14, 45, 15, 15, 15, 15, 15, 15, 7] 150 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000119501366 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000119501366 Building ZINC000049226626 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000049226626 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/650 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000049226626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000049226626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000049226626 none CCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 28, 14, 28, 7, 4, 7, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 28, 14, 14, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/651 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000049226626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000049226626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000049226626 none CCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 28, 14, 28, 7, 4, 7, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 28, 14, 14, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000049226626 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 Building ZINC000049226626 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000049226626 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 650) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000049226626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000049226626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000049226626 none CCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 28, 14, 28, 7, 4, 7, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 28, 14, 14, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 651) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000049226626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000049226626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000049226626 none CCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 28, 14, 28, 7, 4, 7, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 28, 14, 14, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000049226626 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000049226626 Building ZINC000652410025 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652410025 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/652 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ncc[nH]1) `ZINC000652410025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652410025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000652410025 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ncc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 42, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 42, 42] 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]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/653 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ncc[nH]1) `ZINC000652410025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652410025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000652410025 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ncc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 43, 43, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652410025 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 Building ZINC000652410025 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652410025 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 652) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ncc[nH]1) `ZINC000652410025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652410025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000652410025 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ncc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 42, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 42, 42] 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]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 653) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ncc[nH]1) `ZINC000652410025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652410025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000652410025 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ncc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 43, 43, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000652410025 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000652410025 Building ZINC000663123717 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663123717 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/654 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCCCC2)cn1) `ZINC000663123717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663123717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000663123717 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 5, 5, 10, 17, 29, 30, 30, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 5, 29, 29, 90, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 200 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/655 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCCCC2)cn1) `ZINC000663123717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663123717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000663123717 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 5, 5, 10, 17, 30, 33, 33, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 5, 30, 30, 99, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 224 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663123717 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 Building ZINC000663123717 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663123717 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 654) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCCCC2)cn1) `ZINC000663123717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663123717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000663123717 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 5, 5, 10, 17, 29, 30, 30, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 5, 29, 29, 90, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 200 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 655) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCCCC2)cn1) `ZINC000663123717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663123717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000663123717 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 5, 5, 10, 17, 30, 33, 33, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 5, 30, 30, 99, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 224 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663123717 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663123717 Building ZINC000663130322 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663130322 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/656 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(=O)O)CCOC2)cc1) `ZINC000663130322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663130322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000663130322 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(=O)O)CCOC2)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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 6, 6, 1, 1, 1, 1, 7, 7, 13, 27, 37, 37, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 7, 111, 27, 27, 27, 27, 27, 27, 6, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 255 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/657 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(=O)O)CCOC2)cc1) `ZINC000663130322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663130322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000663130322 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(=O)O)CCOC2)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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 8, 8, 13, 27, 38, 38, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 8, 114, 27, 27, 27, 27, 27, 27, 6, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 239 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663130322 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 Building ZINC000663130322 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663130322 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 656) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(=O)O)CCOC2)cc1) `ZINC000663130322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663130322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000663130322 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(=O)O)CCOC2)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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 6, 6, 1, 1, 1, 1, 7, 7, 13, 27, 37, 37, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 7, 111, 27, 27, 27, 27, 27, 27, 6, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 255 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 657) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(=O)O)CCOC2)cc1) `ZINC000663130322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663130322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000663130322 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(=O)O)CCOC2)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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 8, 8, 13, 27, 38, 38, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 8, 114, 27, 27, 27, 27, 27, 27, 6, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 239 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663130322 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130322 Building ZINC000663130323 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663130323 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/658 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(=O)O)CCOC2)cc1) `ZINC000663130323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663130323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000663130323 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(=O)O)CCOC2)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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 12, 27, 38, 38, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 114, 27, 27, 27, 27, 27, 27, 6, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 237 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/659 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(=O)O)CCOC2)cc1) `ZINC000663130323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663130323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000663130323 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(=O)O)CCOC2)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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 6, 6, 1, 1, 1, 1, 7, 7, 12, 29, 36, 36, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 7, 108, 29, 29, 29, 29, 29, 29, 6, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 246 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663130323 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 Building ZINC000663130323 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663130323 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 658) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(=O)O)CCOC2)cc1) `ZINC000663130323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663130323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000663130323 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(=O)O)CCOC2)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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 12, 27, 38, 38, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 114, 27, 27, 27, 27, 27, 27, 6, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 237 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 659) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(=O)O)CCOC2)cc1) `ZINC000663130323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663130323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000663130323 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(=O)O)CCOC2)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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 6, 6, 1, 1, 1, 1, 7, 7, 12, 29, 36, 36, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 7, 108, 29, 29, 29, 29, 29, 29, 6, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 246 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663130323 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663130323 Building ZINC000663138252 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663138252 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/660 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(=O)O) `ZINC000663138252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663138252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000663138252 none CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 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: [37, 37, 36, 31, 13, 32, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 35, 38, 38, 37, 37, 37, 37, 37, 37, 37, 37, 37, 13, 13, 2, 6, 6, 6, 6, 6, 35, 35, 114] 150 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: 329 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/661 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(=O)O) `ZINC000663138252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663138252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000663138252 none CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 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: [37, 37, 36, 32, 14, 33, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 34, 38, 38, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 2, 5, 5, 5, 5, 5, 34, 34, 114] 150 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: 321 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663138252 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 Building ZINC000663138252 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000663138252 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 660) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(=O)O) `ZINC000663138252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000663138252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000663138252 none CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 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: [37, 37, 36, 31, 13, 32, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 35, 38, 38, 37, 37, 37, 37, 37, 37, 37, 37, 37, 13, 13, 2, 6, 6, 6, 6, 6, 35, 35, 114] 150 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: 329 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 661) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(=O)O) `ZINC000663138252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000663138252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000663138252 none CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 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: [37, 37, 36, 32, 14, 33, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 34, 38, 38, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 2, 5, 5, 5, 5, 5, 34, 34, 114] 150 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: 321 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000663138252 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000663138252 Building ZINC000840925804 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840925804 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/662 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)OC[C@H](CNC(=O)[C@@]([O-])([SiH3])C2CCSCC2)O1) `ZINC000840925804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840925804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000840925804 none CC1(C)OC[C@H](CNC(=O)[C@@]([O-])([SiH3])C2CCSCC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 26, 40, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 17, 17, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/663 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)OC[C@H](CNC(=O)[C@]([O-])([SiH3])C2CCSCC2)O1) `ZINC000840925804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840925804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000840925804 none CC1(C)OC[C@H](CNC(=O)[C@]([O-])([SiH3])C2CCSCC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 26, 45, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 17, 17, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000840925804 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 Building ZINC000840925804 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840925804 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 662) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC1(C)OC[C@H](CNC(=O)[C@@]([O-])([SiH3])C2CCSCC2)O1) `ZINC000840925804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840925804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000840925804 none CC1(C)OC[C@H](CNC(=O)[C@@]([O-])([SiH3])C2CCSCC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 26, 40, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 17, 17, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 663) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC1(C)OC[C@H](CNC(=O)[C@]([O-])([SiH3])C2CCSCC2)O1) `ZINC000840925804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840925804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000840925804 none CC1(C)OC[C@H](CNC(=O)[C@]([O-])([SiH3])C2CCSCC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 26, 45, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 17, 17, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000840925804 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840925804 Building ZINC000840926521 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840926521 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/664 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840926521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840926521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926521 none CCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 29, 29, 29, 29, 29, 21, 21, 21, 21, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/665 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840926521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840926521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926521 none CCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 7, 23, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 23, 23, 34, 34, 34, 34, 34, 23, 23, 23, 23, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000840926521 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 Building ZINC000840926521 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840926521 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 664) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840926521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840926521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926521 none CCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 29, 29, 29, 29, 29, 21, 21, 21, 21, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 665) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840926521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840926521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926521 none CCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 7, 23, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 23, 23, 34, 34, 34, 34, 34, 23, 23, 23, 23, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000840926521 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000840926521 Building ZINC000888954761 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000888954761 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/666 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 33, 33, 33, 33, 33, 99, 33, 33, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/667 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 41, 41, 41, 41, 41, 123, 41, 41, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/668 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/668' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 33, 33, 33, 33, 33, 99, 33, 33, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/669 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/669' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 41, 41, 41, 41, 41, 123, 41, 41, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000888954761 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 Building ZINC000888954761 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000888954761 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 666) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 33, 33, 33, 33, 33, 99, 33, 33, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 667) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 41, 41, 41, 41, 41, 123, 41, 41, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 668) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 33, 33, 33, 33, 33, 99, 33, 33, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 669) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 41, 41, 41, 41, 41, 123, 41, 41, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000888954761 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 Building ZINC000888954761 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000888954761 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 666) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 33, 33, 33, 33, 33, 99, 33, 33, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 667) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 41, 41, 41, 41, 41, 123, 41, 41, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 668) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 33, 33, 33, 33, 33, 99, 33, 33, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 669) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 41, 41, 41, 41, 41, 123, 41, 41, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000888954761 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 Building ZINC000888954761 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000888954761 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 666) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 33, 33, 33, 33, 33, 99, 33, 33, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 667) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 41, 41, 41, 41, 41, 123, 41, 41, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 668) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 33, 33, 33, 33, 33, 99, 33, 33, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 669) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954761.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000888954761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954761 none O=C(N[C@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 41, 41, 41, 41, 41, 123, 41, 41, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000888954761 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954761 Building ZINC000888954762 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000888954762 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/670 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 43, 43, 43, 43, 43, 129, 43, 43, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/671 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 36, 36, 36, 36, 36, 108, 36, 36, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/672 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/672' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 43, 43, 43, 43, 43, 129, 43, 43, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/673 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/673' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 36, 36, 36, 36, 36, 108, 36, 36, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000888954762 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 Building ZINC000888954762 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000888954762 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 670) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 43, 43, 43, 43, 43, 129, 43, 43, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 671) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 36, 36, 36, 36, 36, 108, 36, 36, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 672) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 43, 43, 43, 43, 43, 129, 43, 43, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 673) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 36, 36, 36, 36, 36, 108, 36, 36, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000888954762 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 Building ZINC000888954762 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000888954762 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 670) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 43, 43, 43, 43, 43, 129, 43, 43, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 671) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 36, 36, 36, 36, 36, 108, 36, 36, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 672) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 43, 43, 43, 43, 43, 129, 43, 43, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 673) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 36, 36, 36, 36, 36, 108, 36, 36, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000888954762 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 Building ZINC000888954762 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000888954762 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 670) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 43, 43, 43, 43, 43, 129, 43, 43, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 671) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 36, 36, 36, 36, 36, 108, 36, 36, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 672) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 43, 43, 43, 43, 43, 129, 43, 43, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 673) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000888954762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000888954762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000888954762 none O=C(N[C@@H]1CC12CC(O)C2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 36, 36, 36, 36, 36, 108, 36, 36, 6, 6, 12, 6, 6] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000888954762 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000888954762 Building ZINC000165044377 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000165044377 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/674 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000165044377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000165044377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000165044377 none CCOC(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 5, 32, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/675 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000165044377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000165044377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000165044377 none CCOC(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 8, 28, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 5, 5, 5, 5, 5, 8, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000165044377 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 Building ZINC000165044377 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000165044377 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 674) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000165044377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000165044377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000165044377 none CCOC(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 5, 32, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 675) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000165044377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000165044377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000165044377 none CCOC(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 8, 28, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 5, 5, 5, 5, 5, 8, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000165044377 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000165044377 Building ZINC000623053283 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623053283 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/676 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCNC2(CCC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623053283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623053283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623053283 none O=C(N[C@@H]1CCNC2(CCC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 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, 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, 7] 0 hydrogens 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, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 9, 9, 9, 9, 9, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/677 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCNC2(CCC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623053283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623053283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623053283 none O=C(N[C@@H]1CCNC2(CCC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 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, 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, 7] 0 hydrogens 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, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 8, 8, 8, 8, 8, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623053283 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 Building ZINC000623053283 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623053283 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 676) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CCNC2(CCC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623053283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623053283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623053283 none O=C(N[C@@H]1CCNC2(CCC2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 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, 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, 7] 0 hydrogens 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, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 9, 9, 9, 9, 9, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 677) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CCNC2(CCC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623053283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623053283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623053283 none O=C(N[C@@H]1CCNC2(CCC2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', '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, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 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, 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, 7] 0 hydrogens 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, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 8, 8, 8, 8, 8, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623053283 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623053283 Building ZINC000623054564 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623054564 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/678 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCNC2CC2)cn1) `ZINC000623054564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623054564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623054564 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCNC2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 11, 12, 17, 26, 26, 4, 4, 8, 8, 8, 8, 8, 4, 2, 9, 9, 12, 12, 12, 12, 17, 26, 26, 26, 26, 26, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/679 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCCNC2CC2)cn1) `ZINC000623054564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623054564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623054564 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCCNC2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 11, 13, 18, 27, 27, 4, 4, 8, 8, 8, 8, 8, 4, 2, 9, 9, 12, 12, 13, 13, 18, 27, 27, 27, 27, 27, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623054564 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 Building ZINC000623054564 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623054564 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 678) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCNC2CC2)cn1) `ZINC000623054564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623054564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623054564 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCNC2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 11, 12, 17, 26, 26, 4, 4, 8, 8, 8, 8, 8, 4, 2, 9, 9, 12, 12, 12, 12, 17, 26, 26, 26, 26, 26, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 679) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCCCNC2CC2)cn1) `ZINC000623054564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623054564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623054564 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCCNC2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 11, 13, 18, 27, 27, 4, 4, 8, 8, 8, 8, 8, 4, 2, 9, 9, 12, 12, 13, 13, 18, 27, 27, 27, 27, 27, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623054564 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054564 Building ZINC000623054707 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623054707 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/680 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@H](C)N)cn1) `ZINC000623054707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623054707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054707 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [26, 10, 10, 10, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 10, 10, 26, 26, 26, 26, 26, 10, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 10] 47 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/681 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@H](C)N)cn1) `ZINC000623054707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623054707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054707 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 8, 8, 26, 26, 26, 26, 26, 8, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623054707 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 Building ZINC000623054707 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623054707 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 680) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@H](C)N)cn1) `ZINC000623054707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623054707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054707 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [26, 10, 10, 10, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 10, 10, 26, 26, 26, 26, 26, 10, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 10] 47 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 681) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@H](C)N)cn1) `ZINC000623054707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623054707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054707 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 1, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 8, 8, 26, 26, 26, 26, 26, 8, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623054707 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054707 Building ZINC000623054709 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623054709 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/682 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2[C@@H](C)N)cn1) `ZINC000623054709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623054709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054709 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2[C@@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/683 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2[C@@H](C)N)cn1) `ZINC000623054709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623054709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054709 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2[C@@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 9, 9, 9, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 9, 9, 21, 21, 21, 21, 21, 9, 10, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623054709 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 Building ZINC000623054709 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623054709 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 682) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2[C@@H](C)N)cn1) `ZINC000623054709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623054709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054709 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2[C@@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 683) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2[C@@H](C)N)cn1) `ZINC000623054709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623054709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054709 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2[C@@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 9, 9, 9, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 9, 9, 21, 21, 21, 21, 21, 9, 10, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623054709 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054709 Building ZINC000623054710 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623054710 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/684 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@@H](C)N)cn1) `ZINC000623054710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623054710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054710 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 10, 10, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 10, 10, 27, 27, 27, 27, 27, 10, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/685 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@@H](C)N)cn1) `ZINC000623054710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623054710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054710 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 7, 7, 28, 28, 28, 28, 28, 7, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623054710 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 Building ZINC000623054710 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623054710 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 684) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@@H](C)N)cn1) `ZINC000623054710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623054710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054710 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 10, 10, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 10, 10, 27, 27, 27, 27, 27, 10, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 685) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@@H](C)N)cn1) `ZINC000623054710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623054710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623054710 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2[C@@H](C)N)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', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 7, 7, 28, 28, 28, 28, 28, 7, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623054710 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623054710 Building ZINC000623055336 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055336 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/686 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H]2CCCNC2)cn1) `ZINC000623055336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055336 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 7, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 3, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/687 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H]2CCCNC2)cn1) `ZINC000623055336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055336 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 7, 7, 9, 16, 16, 16, 16, 16, 16, 7, 7, 16, 16, 16, 16, 16, 7, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055336 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 Building ZINC000623055336 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055336 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 686) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H]2CCCNC2)cn1) `ZINC000623055336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055336 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 7, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 3, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 687) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H]2CCCNC2)cn1) `ZINC000623055336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055336 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 7, 7, 9, 16, 16, 16, 16, 16, 16, 7, 7, 16, 16, 16, 16, 16, 7, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055336 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055336 Building ZINC000623055337 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055337 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/688 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCNC2)cn1) `ZINC000623055337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055337 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 18, 18, 18, 18, 18, 6, 6, 24, 24, 24, 24, 24, 6, 3, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/689 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCNC2)cn1) `ZINC000623055337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055337 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 16, 16, 16, 16, 16, 16, 6, 6, 18, 18, 18, 18, 18, 6, 3, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055337 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 Building ZINC000623055337 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055337 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 688) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCNC2)cn1) `ZINC000623055337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055337 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 18, 18, 18, 18, 18, 6, 6, 24, 24, 24, 24, 24, 6, 3, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 689) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCNC2)cn1) `ZINC000623055337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055337 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 16, 16, 16, 16, 16, 16, 6, 6, 18, 18, 18, 18, 18, 6, 3, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055337 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055337 Building ZINC000623055338 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055338 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/690 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCNC2)cn1) `ZINC000623055338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055338 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 9, 15, 15, 15, 15, 15, 15, 6, 6, 17, 17, 17, 17, 17, 6, 3, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/691 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCNC2)cn1) `ZINC000623055338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055338 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 8, 14, 14, 14, 14, 14, 14, 6, 6, 23, 23, 23, 23, 23, 6, 2, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055338 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 Building ZINC000623055338 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055338 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 690) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)N[C@@H](C)[C@H]2CCCNC2)cn1) `ZINC000623055338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055338 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 9, 15, 15, 15, 15, 15, 15, 6, 6, 17, 17, 17, 17, 17, 6, 3, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 691) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)N[C@@H](C)[C@H]2CCCNC2)cn1) `ZINC000623055338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055338 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 8, 14, 14, 14, 14, 14, 14, 6, 6, 23, 23, 23, 23, 23, 6, 2, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055338 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055338 Building ZINC000623055339 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055339 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/692 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H]2CCCNC2)cn1) `ZINC000623055339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055339 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 6, 6, 16, 16, 16, 16, 16, 6, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/693 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H]2CCCNC2)cn1) `ZINC000623055339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055339 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 6, 16, 16, 16, 16, 16, 6, 2, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055339 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 Building ZINC000623055339 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055339 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 692) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)N[C@@H](C)[C@@H]2CCCNC2)cn1) `ZINC000623055339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055339 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 6, 6, 16, 16, 16, 16, 16, 6, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 693) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)N[C@@H](C)[C@@H]2CCCNC2)cn1) `ZINC000623055339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623055339 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 6, 16, 16, 16, 16, 16, 6, 2, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055339 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055339 Building ZINC000623055057 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055057 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/694 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN)cn1) `ZINC000623055057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055057 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN)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', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 14, 6, 6, 21, 21, 21, 21, 21, 6, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/695 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN)cn1) `ZINC000623055057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055057 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN)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', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 19, 6, 6, 26, 26, 26, 26, 26, 6, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055057 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 Building ZINC000623055057 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055057 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 694) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)N2CCCC[C@@H]2CN)cn1) `ZINC000623055057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055057 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN)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', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 14, 6, 6, 21, 21, 21, 21, 21, 6, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 695) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)N2CCCC[C@@H]2CN)cn1) `ZINC000623055057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055057 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN)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', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 19, 6, 6, 26, 26, 26, 26, 26, 6, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055057 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055057 Building ZINC000623055058 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055058 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/696 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN)cn1) `ZINC000623055058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055058 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN)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', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 15, 6, 6, 19, 19, 19, 19, 19, 6, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 117 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/697 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN)cn1) `ZINC000623055058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055058 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN)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', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 16, 6, 6, 23, 23, 23, 23, 23, 6, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055058 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 Building ZINC000623055058 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055058 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 696) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)N2CCCC[C@H]2CN)cn1) `ZINC000623055058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055058 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN)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', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 15, 6, 6, 19, 19, 19, 19, 19, 6, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 117 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 697) grep: /scratch/xiaobo/170854/xdl-8058088.90/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)N2CCCC[C@H]2CN)cn1) `ZINC000623055058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055058 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN)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', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 16, 6, 6, 23, 23, 23, 23, 23, 6, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055058 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055058 Building ZINC000623055661 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055661 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/698 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCNC2)cn1) `ZINC000623055661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055661 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 6, 6, 12, 12, 12, 12, 12, 6, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/699 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCNC2)cn1) `ZINC000623055661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055661 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 19, 19, 19, 19, 19, 19, 6, 6, 12, 12, 12, 12, 12, 6, 2, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055661 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 Building ZINC000623055661 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055661 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 698) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCNC2)cn1) `ZINC000623055661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055661 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 6, 6, 12, 12, 12, 12, 12, 6, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 699) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCNC2)cn1) `ZINC000623055661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055661 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 19, 19, 19, 19, 19, 19, 6, 6, 12, 12, 12, 12, 12, 6, 2, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055661 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055661 Building ZINC000623055662 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055662 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/700 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCCNC2)cn1) `ZINC000623055662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055662 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 5, 5, 10, 10, 10, 10, 10, 5, 2, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/701 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCCNC2)cn1) `ZINC000623055662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055662 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 20, 20, 20, 20, 20, 20, 5, 5, 10, 10, 10, 10, 10, 5, 2, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055662 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 Building ZINC000623055662 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055662 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 700) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCCNC2)cn1) `ZINC000623055662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055662 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 5, 5, 10, 10, 10, 10, 10, 5, 2, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 701) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCCNC2)cn1) `ZINC000623055662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055662 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCCNC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 20, 20, 20, 20, 20, 20, 5, 5, 10, 10, 10, 10, 10, 5, 2, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055662 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055662 Building ZINC000623055761 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055761 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/702 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](NC)C2)cn1) `ZINC000623055761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055761 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](NC)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', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 5, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 5, 6, 10, 10, 10, 10, 10, 10, 16, 10, 6, 6, 19, 19, 19, 19, 19, 6, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/703 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](NC)C2)cn1) `ZINC000623055761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055761 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](NC)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', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 5, 1, 8, 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, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 6, 7, 11, 11, 11, 11, 11, 11, 18, 11, 6, 6, 18, 18, 18, 18, 18, 6, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055761 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 Building ZINC000623055761 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055761 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 702) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](NC)C2)cn1) `ZINC000623055761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055761 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](NC)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', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 5, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 5, 6, 10, 10, 10, 10, 10, 10, 16, 10, 6, 6, 19, 19, 19, 19, 19, 6, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 703) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](NC)C2)cn1) `ZINC000623055761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055761 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](NC)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', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 5, 1, 8, 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, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 6, 7, 11, 11, 11, 11, 11, 11, 18, 11, 6, 6, 18, 18, 18, 18, 18, 6, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055761 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055761 Building ZINC000623055762 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055762 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/704 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](NC)C2)cn1) `ZINC000623055762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055762 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](NC)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', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 5, 1, 8, 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, 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] 0 hydrogens 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, 6, 6, 1, 1, 1, 2, 6, 8, 12, 12, 12, 12, 12, 12, 18, 12, 6, 6, 16, 16, 16, 16, 16, 6, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 12, 12, 6] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/705 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](NC)C2)cn1) `ZINC000623055762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055762 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](NC)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', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 5, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 16, 9, 6, 6, 15, 15, 15, 15, 15, 6, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 9, 9, 6] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055762 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 Building ZINC000623055762 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623055762 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 704) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](NC)C2)cn1) `ZINC000623055762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055762 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](NC)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', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 5, 1, 8, 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, 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] 0 hydrogens 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, 6, 6, 1, 1, 1, 2, 6, 8, 12, 12, 12, 12, 12, 12, 18, 12, 6, 6, 16, 16, 16, 16, 16, 6, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 12, 12, 6] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 705) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](NC)C2)cn1) `ZINC000623055762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055762 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](NC)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', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 5, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 16, 9, 6, 6, 15, 15, 15, 15, 15, 6, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 9, 9, 6] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055762 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055762 Building ZINC000623055932 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000623055932 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/706 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/707 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/708 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/708' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/709 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/709' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055932 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 Building ZINC000623055932 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000623055932 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 706) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 707) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 708) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 709) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055932 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 Building ZINC000623055932 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000623055932 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 706) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 707) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 708) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 709) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055932 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 Building ZINC000623055932 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000623055932 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 706) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 707) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 708) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 709) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1) `ZINC000623055932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000623055932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623055932 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H](N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623055932 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623055932 Building ZINC000623056402 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056402 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/710 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC[C@H]2CCCN2)cn1) `ZINC000623056402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056402 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC[C@H]2CCCN2)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 21, 21, 21, 21, 21, 5, 5, 10, 10, 10, 10, 10, 5, 2, 7, 7, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/711 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCC[C@H]2CCCN2)cn1) `ZINC000623056402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056402 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCC[C@H]2CCCN2)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 14, 21, 23, 23, 23, 23, 23, 4, 4, 8, 8, 8, 8, 8, 4, 2, 12, 12, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056402 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 Building ZINC000623056402 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056402 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 710) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC[C@H]2CCCN2)cn1) `ZINC000623056402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056402 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC[C@H]2CCCN2)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 21, 21, 21, 21, 21, 5, 5, 10, 10, 10, 10, 10, 5, 2, 7, 7, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 711) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCC[C@H]2CCCN2)cn1) `ZINC000623056402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056402 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCC[C@H]2CCCN2)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 14, 21, 23, 23, 23, 23, 23, 4, 4, 8, 8, 8, 8, 8, 4, 2, 12, 12, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056402 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056402 Building ZINC000623056403 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056403 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/712 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC[C@@H]2CCCN2)cn1) `ZINC000623056403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056403 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC[C@@H]2CCCN2)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 12, 13, 19, 19, 19, 19, 19, 5, 5, 11, 11, 11, 11, 11, 5, 2, 9, 9, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/713 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCC[C@@H]2CCCN2)cn1) `ZINC000623056403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056403 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCC[C@@H]2CCCN2)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 21, 21, 21, 21, 21, 5, 5, 10, 10, 10, 10, 10, 5, 2, 7, 7, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056403 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 Building ZINC000623056403 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056403 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 712) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC[C@@H]2CCCN2)cn1) `ZINC000623056403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056403 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC[C@@H]2CCCN2)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 12, 13, 19, 19, 19, 19, 19, 5, 5, 11, 11, 11, 11, 11, 5, 2, 9, 9, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 713) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCC[C@@H]2CCCN2)cn1) `ZINC000623056403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056403 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCC[C@@H]2CCCN2)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 21, 21, 21, 21, 21, 5, 5, 10, 10, 10, 10, 10, 5, 2, 7, 7, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056403 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056403 Building ZINC000623056669 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056669 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/714 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/714' -> `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)N)CC2)cn1) `ZINC000623056669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056669 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H](C)N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 14, 14, 14, 8, 8, 5, 5, 13, 13, 13, 13, 13, 5, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/715 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/715' -> `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)N)CC2)cn1) `ZINC000623056669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056669 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@H](C)N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 15, 15, 15, 9, 9, 4, 4, 10, 10, 10, 10, 10, 4, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 9, 9, 9, 9, 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]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056669 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 Building ZINC000623056669 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056669 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 714) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H](C)N)CC2)cn1) `ZINC000623056669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056669 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H](C)N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 14, 14, 14, 8, 8, 5, 5, 13, 13, 13, 13, 13, 5, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 715) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@H](C)N)CC2)cn1) `ZINC000623056669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056669 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@H](C)N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 15, 15, 15, 9, 9, 4, 4, 10, 10, 10, 10, 10, 4, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 9, 9, 9, 9, 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]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056669 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056669 Building ZINC000623056670 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056670 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/716 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/716' -> `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)N)CC2)cn1) `ZINC000623056670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056670 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H](C)N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 6, 7, 7, 7, 7, 14, 14, 14, 7, 7, 4, 4, 10, 10, 10, 10, 10, 4, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 7, 7, 7, 7, 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]) total number of confs: 77 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/717 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/717' -> `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)N)CC2)cn1) `ZINC000623056670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056670 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H](C)N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 16, 16, 16, 8, 8, 4, 4, 10, 10, 10, 10, 10, 4, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 8, 8, 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]) total number of confs: 85 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056670 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 Building ZINC000623056670 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056670 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 716) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H](C)N)CC2)cn1) `ZINC000623056670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056670 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H](C)N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 6, 7, 7, 7, 7, 14, 14, 14, 7, 7, 4, 4, 10, 10, 10, 10, 10, 4, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 7, 7, 7, 7, 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]) total number of confs: 77 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 717) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H](C)N)CC2)cn1) `ZINC000623056670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623056670 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H](C)N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 16, 16, 16, 8, 8, 4, 4, 10, 10, 10, 10, 10, 4, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 8, 8, 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]) total number of confs: 85 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056670 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056670 Building ZINC000623056675 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056675 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/718 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[C@@H]2CCNC2)cn1) `ZINC000623056675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056675 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[C@@H]2CCNC2)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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 12, 18, 21, 21, 21, 21, 5, 5, 13, 13, 13, 13, 13, 5, 2, 8, 8, 12, 12, 21, 21, 21, 21, 21, 21, 21, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/719 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[C@@H]2CCNC2)cn1) `ZINC000623056675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056675 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[C@@H]2CCNC2)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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 10, 15, 18, 18, 18, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 8, 8, 10, 10, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056675 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 Building ZINC000623056675 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056675 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 718) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[C@@H]2CCNC2)cn1) `ZINC000623056675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056675 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[C@@H]2CCNC2)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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 12, 18, 21, 21, 21, 21, 5, 5, 13, 13, 13, 13, 13, 5, 2, 8, 8, 12, 12, 21, 21, 21, 21, 21, 21, 21, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 719) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[C@@H]2CCNC2)cn1) `ZINC000623056675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056675 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[C@@H]2CCNC2)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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 10, 15, 18, 18, 18, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 8, 8, 10, 10, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056675 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056675 Building ZINC000623056676 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056676 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/720 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[C@H]2CCNC2)cn1) `ZINC000623056676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056676 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[C@H]2CCNC2)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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 10, 18, 18, 18, 18, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 8, 8, 10, 10, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/721 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[C@H]2CCNC2)cn1) `ZINC000623056676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056676 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[C@H]2CCNC2)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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 10, 20, 20, 20, 20, 20, 5, 5, 13, 13, 13, 13, 13, 5, 2, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056676 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 Building ZINC000623056676 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056676 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 720) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[C@H]2CCNC2)cn1) `ZINC000623056676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056676 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[C@H]2CCNC2)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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 10, 18, 18, 18, 18, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 8, 8, 10, 10, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 721) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[C@H]2CCNC2)cn1) `ZINC000623056676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056676 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[C@H]2CCNC2)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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 10, 20, 20, 20, 20, 20, 5, 5, 13, 13, 13, 13, 13, 5, 2, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056676 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056676 Building ZINC000623056726 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056726 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/722 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNCCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623056726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000623056726 none CCCNCCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 13, 5, 27, 27, 27, 27, 27, 21, 21, 14, 8, 8, 8, 8, 2, 5, 13, 13, 13, 13, 13, 5] 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: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/723 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNCCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623056726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000623056726 none CCCNCCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 7, 7, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 6, 25, 25, 25, 25, 25, 20, 20, 14, 7, 7, 7, 7, 2, 6, 14, 14, 14, 14, 14, 6] 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056726 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 Building ZINC000623056726 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056726 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 722) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCNCCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623056726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000623056726 none CCCNCCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 13, 5, 27, 27, 27, 27, 27, 21, 21, 14, 8, 8, 8, 8, 2, 5, 13, 13, 13, 13, 13, 5] 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: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 723) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCNCCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623056726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000623056726 none CCCNCCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 7, 7, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 6, 25, 25, 25, 25, 25, 20, 20, 14, 7, 7, 7, 7, 2, 6, 14, 14, 14, 14, 14, 6] 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056726 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056726 Building ZINC000623056745 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056745 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/724 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCNC(C)C)cn1) `ZINC000623056745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623056745 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCNC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 11, 16, 24, 24, 5, 5, 11, 11, 11, 11, 11, 5, 2, 9, 9, 9, 9, 11, 11, 16, 24, 24, 24, 24, 24, 24, 24, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/725 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCCNC(C)C)cn1) `ZINC000623056745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623056745 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCCNC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 10, 11, 17, 28, 28, 5, 5, 11, 11, 11, 11, 11, 5, 2, 9, 9, 10, 10, 11, 11, 17, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056745 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 Building ZINC000623056745 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056745 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 724) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCNC(C)C)cn1) `ZINC000623056745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623056745 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCNC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 11, 16, 24, 24, 5, 5, 11, 11, 11, 11, 11, 5, 2, 9, 9, 9, 9, 11, 11, 16, 24, 24, 24, 24, 24, 24, 24, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 725) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCCCNC(C)C)cn1) `ZINC000623056745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623056745 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCCNC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 10, 11, 17, 28, 28, 5, 5, 11, 11, 11, 11, 11, 5, 2, 9, 9, 10, 10, 11, 11, 17, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056745 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056745 Building ZINC000623056874 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056874 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/726 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](N)c2ccccc2)cn1) `ZINC000623056874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056874 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](N)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 13, 13, 13, 13, 13, 6, 2, 12, 12, 22, 22, 22, 22, 22, 22, 22, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/727 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](N)c2ccccc2)cn1) `ZINC000623056874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056874 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](N)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 14, 14, 14, 14, 14, 6, 2, 11, 11, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056874 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 Building ZINC000623056874 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056874 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 726) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](N)c2ccccc2)cn1) `ZINC000623056874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056874 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](N)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 13, 13, 13, 13, 13, 6, 2, 12, 12, 22, 22, 22, 22, 22, 22, 22, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 727) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](N)c2ccccc2)cn1) `ZINC000623056874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056874 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](N)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 14, 14, 14, 14, 14, 6, 2, 11, 11, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056874 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056874 Building ZINC000623056875 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056875 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/728 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](N)c2ccccc2)cn1) `ZINC000623056875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056875 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](N)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 19, 20, 20, 19, 20, 20, 6, 6, 19, 19, 19, 19, 19, 6, 3, 9, 9, 19, 19, 20, 20, 19, 20, 20, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/729 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](N)c2ccccc2)cn1) `ZINC000623056875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056875 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](N)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 15, 15, 15, 15, 15, 6, 2, 12, 12, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056875 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 Building ZINC000623056875 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623056875 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 728) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](N)c2ccccc2)cn1) `ZINC000623056875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623056875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056875 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](N)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 19, 20, 20, 19, 20, 20, 6, 6, 19, 19, 19, 19, 19, 6, 3, 9, 9, 19, 19, 20, 20, 19, 20, 20, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 729) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](N)c2ccccc2)cn1) `ZINC000623056875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623056875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623056875 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](N)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 15, 15, 15, 15, 15, 6, 2, 12, 12, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623056875 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623056875 Building ZINC000623057371 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057371 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/730 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)C2CC2)cn1) `ZINC000623057371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057371 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 5, 9, 9, 10, 10, 24, 24, 24, 24, 24, 10, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/731 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)C2CC2)cn1) `ZINC000623057371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057371 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 4, 4, 4, 6, 6, 11, 6, 11, 11, 9, 9, 23, 23, 23, 23, 23, 9, 4, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057371 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 Building ZINC000623057371 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057371 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 730) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)C2CC2)cn1) `ZINC000623057371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057371 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 5, 9, 9, 10, 10, 24, 24, 24, 24, 24, 10, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 731) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)C2CC2)cn1) `ZINC000623057371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057371 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 4, 4, 4, 6, 6, 11, 6, 11, 11, 9, 9, 23, 23, 23, 23, 23, 9, 4, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057371 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057371 Building ZINC000623057372 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057372 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/732 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C2CC2)cn1) `ZINC000623057372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057372 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 8, 8, 12, 8, 16, 16, 7, 7, 17, 17, 17, 17, 17, 7, 4, 8, 8, 8, 12, 12, 12, 12, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/733 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C2CC2)cn1) `ZINC000623057372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057372 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 11, 8, 15, 15, 6, 6, 16, 16, 16, 16, 16, 6, 4, 8, 8, 8, 11, 11, 11, 11, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057372 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 Building ZINC000623057372 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057372 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 732) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C2CC2)cn1) `ZINC000623057372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057372 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 8, 8, 12, 8, 16, 16, 7, 7, 17, 17, 17, 17, 17, 7, 4, 8, 8, 8, 12, 12, 12, 12, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 733) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C2CC2)cn1) `ZINC000623057372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057372 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 11, 8, 15, 15, 6, 6, 16, 16, 16, 16, 16, 6, 4, 8, 8, 8, 11, 11, 11, 11, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057372 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057372 Building ZINC000623057389 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057389 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/734 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CNC)CC2)cn1) `ZINC000623057389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623057389 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CNC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 3, 3, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 14, 17, 5, 5, 3, 3, 11, 11, 11, 11, 11, 3, 5, 5, 5, 5, 5, 14, 14, 17, 17, 17, 17, 5, 5, 5, 5, 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]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/735 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CNC)CC2)cn1) `ZINC000623057389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623057389 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CNC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 3, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 13, 14, 4, 4, 3, 3, 11, 11, 11, 11, 11, 3, 4, 4, 4, 4, 4, 13, 13, 14, 14, 14, 14, 4, 4, 4, 4, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057389 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 Building ZINC000623057389 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057389 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 734) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CNC)CC2)cn1) `ZINC000623057389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623057389 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CNC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 3, 3, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 14, 17, 5, 5, 3, 3, 11, 11, 11, 11, 11, 3, 5, 5, 5, 5, 5, 14, 14, 17, 17, 17, 17, 5, 5, 5, 5, 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]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 735) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CNC)CC2)cn1) `ZINC000623057389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623057389 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CNC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 3, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 13, 14, 4, 4, 3, 3, 11, 11, 11, 11, 11, 3, 4, 4, 4, 4, 4, 13, 13, 14, 14, 14, 14, 4, 4, 4, 4, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057389 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057389 Building ZINC000623057508 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057508 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/736 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC(CC)(CC)CN)cn1) `ZINC000623057508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057508 none CCn1cc([C@]([O-])([SiH3])C(=O)NC(CC)(CC)CN)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', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 8, 5, 10, 5, 8, 6, 6, 15, 15, 15, 15, 15, 6, 3, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 8, 8, 8, 8, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/737 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC(CC)(CC)CN)cn1) `ZINC000623057508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057508 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC(CC)(CC)CN)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', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 7, 5, 9, 5, 7, 6, 6, 14, 14, 14, 14, 14, 6, 3, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057508 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 Building ZINC000623057508 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057508 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 736) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC(CC)(CC)CN)cn1) `ZINC000623057508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057508 none CCn1cc([C@]([O-])([SiH3])C(=O)NC(CC)(CC)CN)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', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 8, 5, 10, 5, 8, 6, 6, 15, 15, 15, 15, 15, 6, 3, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 8, 8, 8, 8, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 737) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC(CC)(CC)CN)cn1) `ZINC000623057508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057508 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC(CC)(CC)CN)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', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 7, 5, 9, 5, 7, 6, 6, 14, 14, 14, 14, 14, 6, 3, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057508 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057508 Building ZINC000623057023 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057023 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/738 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CCNC1) `ZINC000623057023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000623057023 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CCNC1 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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 18, 5, 7, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 11, 11, 5, 18, 18, 18, 18, 18, 5, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 131 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/739 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CCNC1) `ZINC000623057023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000623057023 none CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CCNC1 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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 22, 6, 6, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 10, 10, 6, 22, 22, 22, 22, 22, 6, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 134 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057023 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 Building ZINC000623057023 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057023 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 738) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CCNC1) `ZINC000623057023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000623057023 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CCNC1 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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 18, 5, 7, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 11, 11, 5, 18, 18, 18, 18, 18, 5, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 131 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 739) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CCNC1) `ZINC000623057023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000623057023 none CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CCNC1 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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 22, 6, 6, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 10, 10, 6, 22, 22, 22, 22, 22, 6, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 134 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057023 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057023 Building ZINC000623057024 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057024 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/740 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CCNC1) `ZINC000623057024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000623057024 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CCNC1 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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 18, 6, 6, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 10, 10, 6, 18, 18, 18, 18, 18, 6, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 128 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/741 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CCNC1) `ZINC000623057024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000623057024 none CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CCNC1 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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 6, 15, 15, 15, 15, 15, 6, 13, 13, 13, 13, 13, 13, 13] 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]) total number of confs: 122 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057024 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 Building ZINC000623057024 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057024 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 740) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CCNC1) `ZINC000623057024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000623057024 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CCNC1 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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 18, 6, 6, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 10, 10, 6, 18, 18, 18, 18, 18, 6, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 128 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 741) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CCNC1) `ZINC000623057024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000623057024 none CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CCNC1 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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 6, 15, 15, 15, 15, 15, 6, 13, 13, 13, 13, 13, 13, 13] 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]) total number of confs: 122 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057024 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057024 Building ZINC000623057475 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057475 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/742 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CN)CCCC2)cn1) `ZINC000623057475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057475 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CN)CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 11, 11, 11, 1, 1, 1, 1, 5, 5, 9, 9, 11, 9, 9, 9, 9, 11, 11, 31, 31, 31, 31, 31, 11, 5, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 11] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/743 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CN)CCCC2)cn1) `ZINC000623057475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057475 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CN)CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 10, 10, 10, 1, 1, 1, 1, 5, 5, 9, 11, 12, 11, 11, 11, 11, 10, 10, 28, 28, 28, 28, 28, 10, 5, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 10] 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]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057475 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 Building ZINC000623057475 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057475 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 742) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CN)CCCC2)cn1) `ZINC000623057475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057475 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CN)CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 11, 11, 11, 1, 1, 1, 1, 5, 5, 9, 9, 11, 9, 9, 9, 9, 11, 11, 31, 31, 31, 31, 31, 11, 5, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 11] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 743) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CN)CCCC2)cn1) `ZINC000623057475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057475 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CN)CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 10, 10, 10, 1, 1, 1, 1, 5, 5, 9, 11, 12, 11, 11, 11, 11, 10, 10, 28, 28, 28, 28, 28, 10, 5, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 10] 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]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057475 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057475 Building ZINC000623057596 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057596 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/744 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN)cc2)cn1) `ZINC000623057596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057596 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 10, 10, 25, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 16, 16, 25, 25, 25, 25, 16, 16, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/745 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN)cc2)cn1) `ZINC000623057596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057596 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 10, 10, 26, 16, 16, 4, 4, 10, 10, 10, 10, 10, 4, 2, 10, 10, 16, 16, 26, 26, 26, 26, 16, 16, 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057596 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 Building ZINC000623057596 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057596 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 744) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN)cc2)cn1) `ZINC000623057596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057596 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 10, 10, 25, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 16, 16, 25, 25, 25, 25, 16, 16, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 745) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN)cc2)cn1) `ZINC000623057596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623057596 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 10, 10, 26, 16, 16, 4, 4, 10, 10, 10, 10, 10, 4, 2, 10, 10, 16, 16, 26, 26, 26, 26, 16, 16, 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057596 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057596 Building ZINC000623057645 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057645 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/746 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)CC(C)C)cn1) `ZINC000623057645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057645 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 11, 11, 16, 11, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 6, 4, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/747 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)CC(C)C)cn1) `ZINC000623057645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057645 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 12, 9, 15, 15, 15, 6, 6, 22, 22, 22, 22, 22, 6, 3, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057645 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 Building ZINC000623057645 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057645 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 746) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)CC(C)C)cn1) `ZINC000623057645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057645 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 11, 11, 16, 11, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 6, 4, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 747) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)CC(C)C)cn1) `ZINC000623057645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057645 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 12, 9, 15, 15, 15, 6, 6, 22, 22, 22, 22, 22, 6, 3, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057645 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057645 Building ZINC000623057646 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057646 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/748 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)CC(C)C)cn1) `ZINC000623057646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057646 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 7, 9, 9, 9, 10, 10, 30, 30, 30, 30, 30, 10, 3, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10] 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]) total number of confs: 161 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/749 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)CC(C)C)cn1) `ZINC000623057646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057646 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 12, 9, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 3, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 142 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057646 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 Building ZINC000623057646 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057646 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 748) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)CC(C)C)cn1) `ZINC000623057646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057646 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 7, 9, 9, 9, 10, 10, 30, 30, 30, 30, 30, 10, 3, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10] 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]) total number of confs: 161 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 749) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)CC(C)C)cn1) `ZINC000623057646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623057646 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 12, 9, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 3, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 142 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057646 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057646 Building ZINC000623058245 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058245 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/750 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/750' -> `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@@H](C)N)C2)cn1) `ZINC000623058245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058245 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 3, 3, 1, 1, 1, 2, 3, 4, 7, 7, 7, 7, 7, 7, 16, 16, 16, 7, 3, 3, 12, 12, 12, 12, 12, 3, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 7, 7, 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]) total number of confs: 96 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/751 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/751' -> `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@@H](C)N)C2)cn1) `ZINC000623058245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058245 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 2, 2, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 7, 17, 17, 17, 7, 2, 2, 8, 8, 8, 8, 8, 2, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 7, 7, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058245 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 Building ZINC000623058245 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058245 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 750) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@@H](C)N)C2)cn1) `ZINC000623058245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058245 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 3, 3, 1, 1, 1, 2, 3, 4, 7, 7, 7, 7, 7, 7, 16, 16, 16, 7, 3, 3, 12, 12, 12, 12, 12, 3, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 7, 7, 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]) total number of confs: 96 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 751) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@@H](C)N)C2)cn1) `ZINC000623058245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058245 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 2, 2, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 7, 17, 17, 17, 7, 2, 2, 8, 8, 8, 8, 8, 2, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 7, 7, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058245 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058245 Building ZINC000623058246 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058246 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/752 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/752' -> `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@@H](C)N)C2)cn1) `ZINC000623058246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058246 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 2, 4, 5, 7, 7, 7, 7, 7, 7, 20, 20, 20, 7, 4, 4, 11, 11, 11, 11, 11, 4, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 7, 7, 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]) total number of confs: 101 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/753 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/753' -> `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@@H](C)N)C2)cn1) `ZINC000623058246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058246 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 4, 5, 7, 7, 7, 7, 7, 7, 16, 16, 16, 7, 4, 4, 13, 13, 13, 13, 13, 4, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 7, 7, 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]) total number of confs: 93 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058246 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 Building ZINC000623058246 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058246 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 752) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@@H](C)N)C2)cn1) `ZINC000623058246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058246 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 2, 4, 5, 7, 7, 7, 7, 7, 7, 20, 20, 20, 7, 4, 4, 11, 11, 11, 11, 11, 4, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 7, 7, 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]) total number of confs: 101 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 753) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@@H](C)N)C2)cn1) `ZINC000623058246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058246 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 4, 5, 7, 7, 7, 7, 7, 7, 16, 16, 16, 7, 4, 4, 13, 13, 13, 13, 13, 4, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 7, 7, 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]) total number of confs: 93 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058246 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058246 Building ZINC000623058247 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058247 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/754 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/754' -> `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@H](C)N)C2)cn1) `ZINC000623058247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058247 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 3, 3, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 19, 19, 19, 10, 3, 3, 11, 11, 11, 11, 11, 3, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 10, 10, 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]) total number of confs: 97 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/755 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/755' -> `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@H](C)N)C2)cn1) `ZINC000623058247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058247 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 5, 6, 9, 9, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 16, 16, 16, 16, 16, 5, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 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]) total number of confs: 98 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058247 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 Building ZINC000623058247 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058247 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 754) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@H](C)N)C2)cn1) `ZINC000623058247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058247 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 3, 3, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 19, 19, 19, 10, 3, 3, 11, 11, 11, 11, 11, 3, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 10, 10, 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]) total number of confs: 97 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 755) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@H](C)N)C2)cn1) `ZINC000623058247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058247 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]([C@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 5, 6, 9, 9, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 16, 16, 16, 16, 16, 5, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 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]) total number of confs: 98 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058247 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058247 Building ZINC000623058248 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058248 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/756 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/756' -> `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@H](C)N)C2)cn1) `ZINC000623058248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058248 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 1, 1, 1, 2, 4, 5, 8, 8, 8, 8, 8, 8, 15, 15, 15, 8, 4, 4, 10, 10, 10, 10, 10, 4, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 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]) total number of confs: 84 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/757 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/757' -> `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@H](C)N)C2)cn1) `ZINC000623058248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058248 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 3, 3, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 18, 18, 18, 10, 3, 3, 10, 10, 10, 10, 10, 3, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 10, 10, 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]) total number of confs: 93 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058248 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 Building ZINC000623058248 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058248 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 756) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@H](C)N)C2)cn1) `ZINC000623058248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058248 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 1, 1, 1, 2, 4, 5, 8, 8, 8, 8, 8, 8, 15, 15, 15, 8, 4, 4, 10, 10, 10, 10, 10, 4, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 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]) total number of confs: 84 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 757) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@H](C)N)C2)cn1) `ZINC000623058248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058248 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]([C@H](C)N)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', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 3, 3, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 18, 18, 18, 10, 3, 3, 10, 10, 10, 10, 10, 3, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 10, 10, 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]) total number of confs: 93 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058248 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058248 Building ZINC000623058324 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058324 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/758 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N)CCCC2)cn1) `ZINC000623058324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058324 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N)CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 17, 6, 6, 19, 19, 19, 19, 19, 6, 2, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/759 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(N)CCCC2)cn1) `ZINC000623058324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058324 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(N)CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 16, 17, 17, 17, 17, 17, 6, 6, 20, 20, 20, 20, 20, 6, 2, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058324 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 Building ZINC000623058324 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058324 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 758) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N)CCCC2)cn1) `ZINC000623058324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058324 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N)CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 17, 6, 6, 19, 19, 19, 19, 19, 6, 2, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 759) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(N)CCCC2)cn1) `ZINC000623058324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058324 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(N)CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 16, 17, 17, 17, 17, 17, 6, 6, 20, 20, 20, 20, 20, 6, 2, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058324 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058324 Building ZINC000623058332 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058332 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/760 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@@H](C)C2)cn1) `ZINC000623058332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058332 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 9, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 14, 14, 14, 14, 14, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/761 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@@H](C)C2)cn1) `ZINC000623058332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058332 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 10, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 15, 15, 15, 15, 15, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058332 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 Building ZINC000623058332 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058332 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 760) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@@H](C)C2)cn1) `ZINC000623058332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058332 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 9, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 14, 14, 14, 14, 14, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 761) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@@H](C)C2)cn1) `ZINC000623058332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058332 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 10, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 15, 15, 15, 15, 15, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058332 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058332 Building ZINC000623058333 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058333 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/762 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@H](C)C2)cn1) `ZINC000623058333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058333 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 12, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 12, 12, 12, 12, 12, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/763 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@H](C)C2)cn1) `ZINC000623058333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058333 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 16, 16, 16, 16, 16, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058333 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 Building ZINC000623058333 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058333 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 762) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@H](C)C2)cn1) `ZINC000623058333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058333 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 12, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 12, 12, 12, 12, 12, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 763) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@H](C)C2)cn1) `ZINC000623058333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058333 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 16, 16, 16, 16, 16, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058333 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058333 Building ZINC000623058334 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058334 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/764 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@H](C)C2)cn1) `ZINC000623058334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058334 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 2, 8, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 13, 13, 13, 13, 13, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/765 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@H](C)C2)cn1) `ZINC000623058334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058334 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 2, 8, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 14, 14, 14, 14, 14, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058334 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 Building ZINC000623058334 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058334 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 764) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@H](C)C2)cn1) `ZINC000623058334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058334 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 2, 8, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 13, 13, 13, 13, 13, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 765) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@H](C)C2)cn1) `ZINC000623058334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058334 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 2, 8, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 14, 14, 14, 14, 14, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058334 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058334 Building ZINC000623058335 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058335 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/766 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@@H](C)C2)cn1) `ZINC000623058335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058335 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 7, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 19, 19, 19, 19, 19, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/767 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@@H](C)C2)cn1) `ZINC000623058335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058335 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 7, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 15, 15, 15, 15, 15, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058335 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 Building ZINC000623058335 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058335 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 766) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@@H](C)C2)cn1) `ZINC000623058335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058335 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 7, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 19, 19, 19, 19, 19, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 767) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@@H](C)C2)cn1) `ZINC000623058335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623058335 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 7, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 15, 15, 15, 15, 15, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058335 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058335 Building ZINC000623058340 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058340 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/768 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC2CCNCC2)cn1) `ZINC000623058340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058340 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC2CCNCC2)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 20, 26, 26, 26, 26, 26, 4, 4, 8, 8, 8, 8, 8, 4, 2, 14, 14, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/769 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCC2CCNCC2)cn1) `ZINC000623058340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058340 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCC2CCNCC2)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 19, 27, 27, 27, 27, 27, 4, 4, 11, 11, 11, 11, 11, 4, 2, 13, 13, 19, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058340 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 Building ZINC000623058340 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058340 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 768) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC2CCNCC2)cn1) `ZINC000623058340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058340 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC2CCNCC2)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 20, 26, 26, 26, 26, 26, 4, 4, 8, 8, 8, 8, 8, 4, 2, 14, 14, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 769) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCCC2CCNCC2)cn1) `ZINC000623058340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058340 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCC2CCNCC2)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 19, 27, 27, 27, 27, 27, 4, 4, 11, 11, 11, 11, 11, 4, 2, 13, 13, 19, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058340 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058340 Building ZINC000623057860 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057860 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/770 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCNC3)CC2)cn1) `ZINC000623057860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623057860 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCNC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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] 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] 0 hydrogens 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, 1, 1, 1, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 15, 5, 5, 12, 12, 12, 12, 12, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/771 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCNC3)CC2)cn1) `ZINC000623057860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623057860 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCNC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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] 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] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 14, 6, 6, 16, 16, 16, 16, 16, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057860 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 Building ZINC000623057860 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057860 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 770) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCNC3)CC2)cn1) `ZINC000623057860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623057860 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCNC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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] 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] 0 hydrogens 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, 1, 1, 1, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 15, 5, 5, 12, 12, 12, 12, 12, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 771) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCNC3)CC2)cn1) `ZINC000623057860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623057860 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCNC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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] 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] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 14, 6, 6, 16, 16, 16, 16, 16, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057860 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057860 Building ZINC000623057907 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057907 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/772 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCNC2)CC1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623057907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623057907 none O=C(N1CCC2(CCNC2)CC1)[C@]([O-])([SiH3])c1ccc[nH]1 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.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 15, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6] 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: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/773 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCNC2)CC1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623057907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623057907 none O=C(N1CCC2(CCNC2)CC1)[C@@]([O-])([SiH3])c1ccc[nH]1 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.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 5] 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057907 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 Building ZINC000623057907 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623057907 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 772) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N1CCC2(CCNC2)CC1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623057907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623057907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623057907 none O=C(N1CCC2(CCNC2)CC1)[C@]([O-])([SiH3])c1ccc[nH]1 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.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 15, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6] 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: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 773) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N1CCC2(CCNC2)CC1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623057907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623057907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623057907 none O=C(N1CCC2(CCNC2)CC1)[C@@]([O-])([SiH3])c1ccc[nH]1 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.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 5] 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623057907 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623057907 Building ZINC000623058456 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058456 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/774 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](N)C(C)C)cn1) `ZINC000623058456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623058456 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](N)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 17, 17, 17, 22, 22, 6, 6, 17, 17, 17, 17, 17, 6, 3, 11, 11, 17, 17, 22, 22, 22, 22, 22, 22, 22, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/775 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](N)C(C)C)cn1) `ZINC000623058456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623058456 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](N)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 12, 12, 12, 19, 19, 6, 6, 16, 16, 16, 16, 16, 6, 3, 8, 8, 12, 12, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058456 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 Building ZINC000623058456 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058456 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 774) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](N)C(C)C)cn1) `ZINC000623058456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623058456 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](N)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 17, 17, 17, 22, 22, 6, 6, 17, 17, 17, 17, 17, 6, 3, 11, 11, 17, 17, 22, 22, 22, 22, 22, 22, 22, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 775) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](N)C(C)C)cn1) `ZINC000623058456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623058456 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](N)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 12, 12, 12, 19, 19, 6, 6, 16, 16, 16, 16, 16, 6, 3, 8, 8, 12, 12, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058456 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058456 Building ZINC000623058457 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058457 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/776 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](N)C(C)C)cn1) `ZINC000623058457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623058457 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](N)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 14, 14, 6, 6, 14, 14, 14, 14, 14, 6, 2, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/777 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](N)C(C)C)cn1) `ZINC000623058457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623058457 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](N)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 15, 18, 18, 6, 6, 18, 18, 18, 18, 18, 6, 2, 13, 13, 17, 17, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058457 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 Building ZINC000623058457 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058457 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 776) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](N)C(C)C)cn1) `ZINC000623058457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623058457 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](N)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 14, 14, 6, 6, 14, 14, 14, 14, 14, 6, 2, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 777) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](N)C(C)C)cn1) `ZINC000623058457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623058457 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](N)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 15, 18, 18, 6, 6, 18, 18, 18, 18, 18, 6, 2, 13, 13, 17, 17, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058457 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058457 Building ZINC000623059038 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059038 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/778 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N) `ZINC000623059038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059038 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 4, 4, 4, 4, 11, 4, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 12, 12, 4, 11, 11, 11, 11, 11, 4, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 85 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/779 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N) `ZINC000623059038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059038 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 13, 9, 2, 9, 1, 1, 1, 4, 4, 4, 4, 10, 4, 13, 13, 13, 13, 13, 16, 16, 16, 16, 16, 13, 13, 4, 10, 10, 10, 10, 10, 4, 13, 13, 13, 13, 13, 13] 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]) total number of confs: 78 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059038 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 Building ZINC000623059038 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059038 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 778) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N) `ZINC000623059038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059038 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 4, 4, 4, 4, 11, 4, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 12, 12, 4, 11, 11, 11, 11, 11, 4, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 85 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 779) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N) `ZINC000623059038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059038 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 13, 9, 2, 9, 1, 1, 1, 4, 4, 4, 4, 10, 4, 13, 13, 13, 13, 13, 16, 16, 16, 16, 16, 13, 13, 4, 10, 10, 10, 10, 10, 4, 13, 13, 13, 13, 13, 13] 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]) total number of confs: 78 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059038 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059038 Building ZINC000623059039 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059039 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/780 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N) `ZINC000623059039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059039 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 8, 1, 1, 1, 5, 5, 5, 5, 16, 5, 11, 11, 11, 11, 11, 15, 15, 15, 15, 15, 11, 11, 5, 16, 16, 16, 16, 16, 5, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/781 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N) `ZINC000623059039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059039 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 6, 2, 7, 1, 1, 1, 6, 6, 6, 6, 13, 6, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 10, 10, 6, 13, 13, 13, 13, 13, 6, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 83 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059039 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 Building ZINC000623059039 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059039 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 780) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N) `ZINC000623059039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059039 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 8, 1, 1, 1, 5, 5, 5, 5, 16, 5, 11, 11, 11, 11, 11, 15, 15, 15, 15, 15, 11, 11, 5, 16, 16, 16, 16, 16, 5, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 781) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N) `ZINC000623059039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059039 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 6, 2, 7, 1, 1, 1, 6, 6, 6, 6, 13, 6, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 10, 10, 6, 13, 13, 13, 13, 13, 6, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 83 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059039 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059039 Building ZINC000623059040 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059040 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/782 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N) `ZINC000623059040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059040 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 4, 4, 4, 4, 13, 4, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11, 4, 13, 13, 13, 13, 13, 4, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 101 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/783 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N) `ZINC000623059040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059040 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 8, 2, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12, 2, 8, 8, 8, 8, 8, 2, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 81 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059040 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 Building ZINC000623059040 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059040 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 782) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N) `ZINC000623059040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059040 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 4, 4, 4, 4, 13, 4, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11, 4, 13, 13, 13, 13, 13, 4, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 101 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 783) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N) `ZINC000623059040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059040 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 8, 2, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12, 2, 8, 8, 8, 8, 8, 2, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 81 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059040 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059040 Building ZINC000623059041 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059041 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/784 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N) `ZINC000623059041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059041 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 11, 3, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 10, 10, 3, 11, 11, 11, 11, 11, 3, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 84 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/785 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N) `ZINC000623059041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059041 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 11, 3, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 10, 10, 3, 11, 11, 11, 11, 11, 3, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 86 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059041 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 Building ZINC000623059041 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059041 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 784) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N) `ZINC000623059041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059041 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 11, 3, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 10, 10, 3, 11, 11, 11, 11, 11, 3, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 84 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 785) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N) `ZINC000623059041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623059041 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CC[C@H]1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 5, 7, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 11, 3, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 10, 10, 3, 11, 11, 11, 11, 11, 3, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 86 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059041 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059041 Building ZINC000623059312 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059312 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/786 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)CC(C)C)cn1) `ZINC000623059312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623059312 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 1, 1, 1, 1, 6, 6, 6, 8, 8, 9, 8, 8, 8, 8, 12, 12, 26, 26, 26, 26, 26, 12, 6, 8, 8, 8, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12] 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/787 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)CC(C)C)cn1) `ZINC000623059312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623059312 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 8, 8, 9, 8, 8, 8, 8, 9, 9, 19, 19, 19, 19, 19, 9, 6, 8, 8, 8, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9] 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: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059312 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 Building ZINC000623059312 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059312 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 786) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)CC(C)C)cn1) `ZINC000623059312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623059312 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 1, 1, 1, 1, 6, 6, 6, 8, 8, 9, 8, 8, 8, 8, 12, 12, 26, 26, 26, 26, 26, 12, 6, 8, 8, 8, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12] 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 787) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)CC(C)C)cn1) `ZINC000623059312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623059312 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 8, 8, 9, 8, 8, 8, 8, 9, 9, 19, 19, 19, 19, 19, 9, 6, 8, 8, 8, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9] 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: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059312 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059312 Building ZINC000623059313 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059313 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/788 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)CC(C)C)cn1) `ZINC000623059313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623059313 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 8, 8, 10, 8, 8, 8, 8, 10, 10, 21, 21, 21, 21, 21, 10, 5, 8, 8, 8, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10] 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: 114 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/789 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)CC(C)C)cn1) `ZINC000623059313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623059313 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 9, 9, 12, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 9, 5, 9, 9, 9, 12, 12, 12, 12, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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: 116 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059313 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 Building ZINC000623059313 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059313 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 788) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)CC(C)C)cn1) `ZINC000623059313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623059313 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 8, 8, 10, 8, 8, 8, 8, 10, 10, 21, 21, 21, 21, 21, 10, 5, 8, 8, 8, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10] 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: 114 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 789) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)CC(C)C)cn1) `ZINC000623059313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623059313 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 9, 9, 12, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 9, 5, 9, 9, 9, 12, 12, 12, 12, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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: 116 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059313 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059313 Building ZINC000623059317 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059317 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/790 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@H]2C)cn1) `ZINC000623059317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059317 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 16, 16, 16, 16, 16, 6, 2, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/791 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@H]2C)cn1) `ZINC000623059317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059317 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [18, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 18, 18, 18, 18, 18, 6, 3, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059317 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 Building ZINC000623059317 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059317 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 790) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@H]2C)cn1) `ZINC000623059317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059317 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 16, 16, 16, 16, 16, 6, 2, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 791) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@H]2C)cn1) `ZINC000623059317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059317 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [18, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 18, 18, 18, 18, 18, 6, 3, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059317 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059317 Building ZINC000623059318 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059318 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/792 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@@H]2C)cn1) `ZINC000623059318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059318 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 17, 17, 17, 17, 17, 6, 3, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/793 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@@H]2C)cn1) `ZINC000623059318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059318 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [17, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 17, 17, 17, 17, 17, 7, 2, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059318 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 Building ZINC000623059318 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059318 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 792) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@@H]2C)cn1) `ZINC000623059318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059318 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 17, 17, 17, 17, 17, 6, 3, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 793) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@@H]2C)cn1) `ZINC000623059318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059318 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [17, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 17, 17, 17, 17, 17, 7, 2, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059318 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059318 Building ZINC000623059319 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059319 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/794 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@@H]2C)cn1) `ZINC000623059319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059319 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 16, 16, 16, 16, 16, 6, 2, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/795 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@@H]2C)cn1) `ZINC000623059319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059319 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 15, 15, 15, 15, 15, 6, 2, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059319 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 Building ZINC000623059319 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059319 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 794) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@@H]2C)cn1) `ZINC000623059319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059319 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 16, 16, 16, 16, 16, 6, 2, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 795) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@@H]2C)cn1) `ZINC000623059319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059319 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2NC(C)(C)O[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 15, 15, 15, 15, 15, 6, 2, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059319 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059319 Building ZINC000623059320 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059320 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/796 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@H]2C)cn1) `ZINC000623059320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059320 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 16, 16, 16, 16, 16, 6, 2, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/797 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@H]2C)cn1) `ZINC000623059320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059320 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 17, 17, 17, 17, 17, 6, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059320 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 Building ZINC000623059320 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623059320 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 796) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@H]2C)cn1) `ZINC000623059320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623059320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059320 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 16, 16, 16, 16, 16, 6, 2, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 797) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@H]2C)cn1) `ZINC000623059320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623059320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623059320 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2NC(C)(C)O[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 10, 5, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 17, 17, 17, 17, 17, 6, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623059320 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623059320 Building ZINC000188533303 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188533303 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/798 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@H]1C) `ZINC000188533303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188533303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000188533303 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 2, 7, 7, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 16 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/799 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@H]1C) `ZINC000188533303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188533303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000188533303 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 18 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000188533303 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 Building ZINC000188533303 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188533303 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 798) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@H]1C) `ZINC000188533303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188533303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000188533303 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 2, 7, 7, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 16 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 799) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@H]1C) `ZINC000188533303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188533303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000188533303 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 18 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000188533303 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533303 Building ZINC000188533324 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188533324 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/800 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@@H]1C) `ZINC000188533324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188533324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000188533324 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 18 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/801 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@@H]1C) `ZINC000188533324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188533324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000188533324 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 15 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000188533324 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 Building ZINC000188533324 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188533324 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 800) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@@H]1C) `ZINC000188533324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188533324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000188533324 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 18 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 801) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@@H]1C) `ZINC000188533324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188533324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000188533324 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 15 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000188533324 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000188533324 Building ZINC000623058504 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058504 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/802 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058504 none C[C@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 40, 40, 40, 25, 40, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 22, 22, 5, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/803 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058504 none C[C@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 40, 40, 40, 26, 40, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 21, 21, 5, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058504 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 Building ZINC000623058504 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058504 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 802) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058504 none C[C@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 40, 40, 40, 25, 40, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 22, 22, 5, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 803) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058504 none C[C@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 40, 40, 40, 26, 40, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 21, 21, 5, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058504 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058504 Building ZINC000623058506 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058506 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/804 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058506 none C[C@@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 40, 40, 40, 28, 40, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 24, 24, 5, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/805 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058506 none C[C@@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 36, 36, 36, 24, 36, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 20, 20, 5, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058506 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 Building ZINC000623058506 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058506 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 804) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058506 none C[C@@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 40, 40, 40, 28, 40, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 24, 24, 5, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 805) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058506 none C[C@@H]1OC(C)(C)N[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 36, 36, 36, 24, 36, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 20, 20, 5, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058506 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058506 Building ZINC000623058505 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058505 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/806 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OC(C)(C)N[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058505 none C[C@H]1OC(C)(C)N[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 40, 40, 40, 29, 40, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 21, 21, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/807 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OC(C)(C)N[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058505 none C[C@H]1OC(C)(C)N[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 38, 38, 38, 38, 29, 38, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 18, 18, 4, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058505 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 Building ZINC000623058505 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058505 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 806) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1OC(C)(C)N[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058505 none C[C@H]1OC(C)(C)N[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 40, 40, 40, 29, 40, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 21, 21, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 807) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1OC(C)(C)N[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058505 none C[C@H]1OC(C)(C)N[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 38, 38, 38, 38, 29, 38, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 18, 18, 4, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058505 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058505 Building ZINC000623058507 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058507 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/808 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OC(C)(C)N[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058507 none C[C@@H]1OC(C)(C)N[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 39, 39, 39, 24, 39, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 17, 17, 4, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/809 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OC(C)(C)N[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058507 none C[C@@H]1OC(C)(C)N[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 39, 39, 39, 24, 39, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 21, 21, 4, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058507 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 Building ZINC000623058507 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058507 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 808) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1OC(C)(C)N[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058507 none C[C@@H]1OC(C)(C)N[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 39, 39, 39, 24, 39, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 17, 17, 4, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 809) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1OC(C)(C)N[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623058507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000623058507 none C[C@@H]1OC(C)(C)N[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 39, 39, 39, 24, 39, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 21, 21, 4, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058507 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058507 Building ZINC000623058530 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058530 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/810 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2CN)cn1) `ZINC000623058530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058530 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 16, 5, 5, 13, 13, 13, 13, 13, 5, 2, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 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]) total number of confs: 113 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/811 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2CN)cn1) `ZINC000623058530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058530 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 15, 6, 6, 13, 13, 13, 13, 13, 6, 2, 10, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058530 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 Building ZINC000623058530 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058530 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 810) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2CN)cn1) `ZINC000623058530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058530 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 16, 5, 5, 13, 13, 13, 13, 13, 5, 2, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 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]) total number of confs: 113 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 811) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2CN)cn1) `ZINC000623058530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058530 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 15, 6, 6, 13, 13, 13, 13, 13, 6, 2, 10, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058530 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058530 Building ZINC000623058531 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058531 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/812 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2CN)cn1) `ZINC000623058531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058531 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 11, 8, 8, 22, 22, 22, 22, 22, 8, 3, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/813 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2CN)cn1) `ZINC000623058531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058531 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 12, 9, 9, 22, 22, 22, 22, 22, 9, 3, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058531 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 Building ZINC000623058531 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058531 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 812) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2CN)cn1) `ZINC000623058531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058531 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 11, 8, 8, 22, 22, 22, 22, 22, 8, 3, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 813) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2CN)cn1) `ZINC000623058531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058531 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 12, 9, 9, 22, 22, 22, 22, 22, 9, 3, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058531 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058531 Building ZINC000623058532 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058532 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/814 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2CN)cn1) `ZINC000623058532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058532 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 16, 6, 6, 14, 14, 14, 14, 14, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/815 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2CN)cn1) `ZINC000623058532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058532 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 15, 6, 6, 16, 16, 16, 16, 16, 6, 2, 10, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058532 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 Building ZINC000623058532 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058532 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 814) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2CN)cn1) `ZINC000623058532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058532 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 16, 6, 6, 14, 14, 14, 14, 14, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 815) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2CN)cn1) `ZINC000623058532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058532 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 15, 6, 6, 16, 16, 16, 16, 16, 6, 2, 10, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058532 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058532 Building ZINC000623058533 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058533 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/816 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2CN)cn1) `ZINC000623058533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058533 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 15, 6, 6, 16, 16, 16, 16, 16, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/817 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2CN)cn1) `ZINC000623058533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058533 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 16, 6, 6, 15, 15, 15, 15, 15, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058533 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 Building ZINC000623058533 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058533 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 816) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2CN)cn1) `ZINC000623058533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058533 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 15, 6, 6, 16, 16, 16, 16, 16, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 817) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2CN)cn1) `ZINC000623058533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623058533 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2CN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 16, 6, 6, 15, 15, 15, 15, 15, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058533 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058533 Building ZINC001342229231 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342229231 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/818 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2COCCN2)c1) `ZINC001342229231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342229231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001342229231 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2COCCN2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 17, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 1, 6, 6, 4, 17, 17, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/819 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2COCCN2)c1) `ZINC001342229231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342229231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001342229231 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2COCCN2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 1, 6, 6, 3, 18, 18, 32, 32, 32, 32, 32, 32, 32, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001342229231 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 Building ZINC001342229231 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342229231 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 818) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2COCCN2)c1) `ZINC001342229231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342229231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001342229231 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2COCCN2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 17, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 1, 6, 6, 4, 17, 17, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 819) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2COCCN2)c1) `ZINC001342229231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342229231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001342229231 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2COCCN2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 1, 6, 6, 3, 18, 18, 32, 32, 32, 32, 32, 32, 32, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001342229231 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229231 Building ZINC001342229233 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342229233 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/820 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2COCCN2)c1) `ZINC001342229233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342229233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001342229233 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2COCCN2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 20, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 2, 6, 6, 3, 13, 13, 26, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/821 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2COCCN2)c1) `ZINC001342229233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342229233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001342229233 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2COCCN2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 24, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 1, 6, 6, 3, 15, 15, 29, 29, 29, 29, 29, 29, 29, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001342229233 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 Building ZINC001342229233 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342229233 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 820) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2COCCN2)c1) `ZINC001342229233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342229233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001342229233 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2COCCN2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 20, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 2, 6, 6, 3, 13, 13, 26, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 821) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2COCCN2)c1) `ZINC001342229233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342229233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001342229233 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2COCCN2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 24, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 1, 6, 6, 3, 15, 15, 29, 29, 29, 29, 29, 29, 29, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC001342229233 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC001342229233 Building ZINC000623058625 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058625 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/822 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)C(C)C)cn1) `ZINC000623058625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623058625 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 7, 7, 13, 7, 11, 11, 9, 9, 21, 21, 21, 21, 21, 9, 4, 7, 7, 7, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11, 9] 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]) total number of confs: 147 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/823 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)C(C)C)cn1) `ZINC000623058625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623058625 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 13, 7, 11, 11, 7, 7, 17, 17, 17, 17, 17, 7, 4, 7, 7, 7, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058625 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 Building ZINC000623058625 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058625 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 822) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)C(C)C)cn1) `ZINC000623058625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623058625 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CN)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 7, 7, 13, 7, 11, 11, 9, 9, 21, 21, 21, 21, 21, 9, 4, 7, 7, 7, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11, 9] 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]) total number of confs: 147 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 823) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)C(C)C)cn1) `ZINC000623058625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623058625 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CN)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 13, 7, 11, 11, 7, 7, 17, 17, 17, 17, 17, 7, 4, 7, 7, 7, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058625 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058625 Building ZINC000623058626 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058626 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/824 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C(C)C)cn1) `ZINC000623058626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623058626 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 9, 9, 11, 9, 9, 9, 10, 10, 25, 25, 25, 25, 25, 10, 5, 9, 9, 9, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 10] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/825 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C(C)C)cn1) `ZINC000623058626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623058626 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 8, 8, 11, 8, 8, 8, 10, 10, 25, 25, 25, 25, 25, 10, 4, 8, 8, 8, 11, 11, 11, 11, 8, 8, 8, 8, 8, 8, 8, 10] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058626 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 Building ZINC000623058626 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058626 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 824) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C(C)C)cn1) `ZINC000623058626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623058626 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 9, 9, 11, 9, 9, 9, 10, 10, 25, 25, 25, 25, 25, 10, 5, 9, 9, 9, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 10] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 825) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C(C)C)cn1) `ZINC000623058626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623058626 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CN)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 8, 8, 11, 8, 8, 8, 10, 10, 25, 25, 25, 25, 25, 10, 4, 8, 8, 8, 11, 11, 11, 11, 8, 8, 8, 8, 8, 8, 8, 10] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058626 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058626 Building ZINC000623058782 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058782 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/826 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CCNC)CC2)cn1) `ZINC000623058782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000623058782 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CCNC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 14, 18, 21, 5, 5, 2, 2, 7, 7, 7, 7, 7, 2, 5, 5, 5, 5, 5, 14, 14, 18, 18, 21, 21, 21, 21, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/827 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CCNC)CC2)cn1) `ZINC000623058782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000623058782 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CCNC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 3, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 13, 17, 20, 4, 4, 3, 3, 8, 8, 8, 8, 8, 3, 4, 4, 4, 4, 4, 13, 13, 17, 17, 20, 20, 20, 20, 4, 4, 4, 4, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058782 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 Building ZINC000623058782 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058782 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 826) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CCNC)CC2)cn1) `ZINC000623058782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000623058782 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CCNC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 14, 18, 21, 5, 5, 2, 2, 7, 7, 7, 7, 7, 2, 5, 5, 5, 5, 5, 14, 14, 18, 18, 21, 21, 21, 21, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 827) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CCNC)CC2)cn1) `ZINC000623058782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000623058782 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(CCNC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 3, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 13, 17, 20, 4, 4, 3, 3, 8, 8, 8, 8, 8, 3, 4, 4, 4, 4, 4, 13, 13, 17, 17, 20, 20, 20, 20, 4, 4, 4, 4, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058782 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058782 Building ZINC000623058816 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058816 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/828 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@H]3C2)cn1) `ZINC000623058816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058816 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 20, 20, 20, 20, 20, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/829 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@H]3C2)cn1) `ZINC000623058816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058816 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 21, 21, 21, 21, 21, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058816 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 Building ZINC000623058816 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058816 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 828) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@H]3C2)cn1) `ZINC000623058816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058816 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 20, 20, 20, 20, 20, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 829) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@H]3C2)cn1) `ZINC000623058816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058816 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 21, 21, 21, 21, 21, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058816 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058816 Building ZINC000623058817 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058817 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/830 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@@H]3C2)cn1) `ZINC000623058817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058817 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 7, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 17, 17, 17, 17, 17, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/831 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@@H]3C2)cn1) `ZINC000623058817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058817 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 7, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 21, 21, 21, 21, 21, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058817 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 Building ZINC000623058817 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058817 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 830) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@@H]3C2)cn1) `ZINC000623058817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058817 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 7, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 17, 17, 17, 17, 17, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 831) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@@H]3C2)cn1) `ZINC000623058817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058817 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NCC[C@@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 7, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 21, 21, 21, 21, 21, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058817 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058817 Building ZINC000623058818 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058818 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/832 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NCC[C@@H]3C2)cn1) `ZINC000623058818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058818 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NCC[C@@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 2, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 18, 18, 18, 18, 18, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/833 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NCC[C@@H]3C2)cn1) `ZINC000623058818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058818 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NCC[C@@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 23, 23, 23, 23, 23, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058818 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 Building ZINC000623058818 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623058818 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 832) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NCC[C@@H]3C2)cn1) `ZINC000623058818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623058818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058818 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NCC[C@@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 2, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 18, 18, 18, 18, 18, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 833) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NCC[C@@H]3C2)cn1) `ZINC000623058818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623058818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623058818 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NCC[C@@H]3C2)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', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 23, 23, 23, 23, 23, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623058818 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623058818 Building ZINC000623061430 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623061430 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/834 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@@H]2C)cn1) `ZINC000623061430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623061430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061430 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 4, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 20, 20, 20, 20, 20, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/835 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@@H]2C)cn1) `ZINC000623061430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623061430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061430 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 4, 10, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623061430 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 Building ZINC000623061430 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623061430 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 834) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@@H]2C)cn1) `ZINC000623061430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623061430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061430 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 4, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 20, 20, 20, 20, 20, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 835) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@@H]2C)cn1) `ZINC000623061430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623061430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061430 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 4, 10, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623061430 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061430 Building ZINC000623061431 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623061431 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/836 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@H]2C)cn1) `ZINC000623061431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623061431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061431 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 3, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 21, 21, 21, 21, 21, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/837 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@H]2C)cn1) `ZINC000623061431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623061431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061431 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 23, 23, 23, 23, 23, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623061431 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 Building ZINC000623061431 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623061431 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 836) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@H]2C)cn1) `ZINC000623061431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623061431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061431 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 3, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 21, 21, 21, 21, 21, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 837) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@H]2C)cn1) `ZINC000623061431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623061431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061431 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 23, 23, 23, 23, 23, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623061431 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061431 Building ZINC000623061432 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623061432 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/838 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@H]2C)cn1) `ZINC000623061432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623061432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061432 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 10, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/839 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@H]2C)cn1) `ZINC000623061432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623061432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061432 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623061432 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 Building ZINC000623061432 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623061432 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 838) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@H]2C)cn1) `ZINC000623061432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623061432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061432 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 10, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 839) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@H]2C)cn1) `ZINC000623061432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623061432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061432 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623061432 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061432 Building ZINC000623061433 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623061433 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/840 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@@H]2C)cn1) `ZINC000623061433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623061433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061433 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 26, 26, 26, 26, 26, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/841 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@@H]2C)cn1) `ZINC000623061433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623061433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061433 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 11, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 16, 16, 16, 16, 16, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623061433 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 Building ZINC000623061433 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623061433 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 840) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@@H]2C)cn1) `ZINC000623061433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623061433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061433 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 26, 26, 26, 26, 26, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 841) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@@H]2C)cn1) `ZINC000623061433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623061433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623061433 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 11, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 16, 16, 16, 16, 16, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623061433 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623061433 Building ZINC000623060888 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623060888 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/842 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CCNC3)C2)cn1) `ZINC000623060888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623060888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623060888 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CCNC3)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 5, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 15, 15, 15, 15, 15, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/843 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CCNC3)C2)cn1) `ZINC000623060888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623060888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623060888 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CCNC3)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 4, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 14, 14, 14, 14, 14, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623060888 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 Building ZINC000623060888 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623060888 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 842) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CCNC3)C2)cn1) `ZINC000623060888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623060888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623060888 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CCNC3)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 5, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 15, 15, 15, 15, 15, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 843) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CCNC3)C2)cn1) `ZINC000623060888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623060888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623060888 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CCNC3)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 4, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 14, 14, 14, 14, 14, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623060888 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623060888 Building ZINC000623062108 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062108 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/844 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3CC[C@@H](C2)N3)cn1) `ZINC000623062108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623062108 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3CC[C@@H](C2)N3)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 19, 19, 19, 19, 19, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/845 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3CC[C@@H](C2)N3)cn1) `ZINC000623062108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623062108 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3CC[C@@H](C2)N3)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 8, 8, 8, 1, 1, 1, 2, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 24, 24, 24, 24, 24, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 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]) total number of confs: 102 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062108 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 Building ZINC000623062108 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062108 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 844) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3CC[C@@H](C2)N3)cn1) `ZINC000623062108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623062108 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3CC[C@@H](C2)N3)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 19, 19, 19, 19, 19, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 845) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3CC[C@@H](C2)N3)cn1) `ZINC000623062108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 Warning: atom stereo specified for planar atom 22 Warning: atom stereo specified for planar atom 23 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623062108 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3CC[C@@H](C2)N3)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 8, 8, 8, 1, 1, 1, 2, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 24, 24, 24, 24, 24, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 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]) total number of confs: 102 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062108 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062108 Building ZINC000623062533 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062533 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/846 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)C2CCCC2)cn1) `ZINC000623062533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062533 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)C2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 9, 9, 13, 12, 16, 16, 16, 16, 7, 7, 23, 23, 23, 23, 23, 7, 3, 13, 13, 13, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/847 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)C2CCCC2)cn1) `ZINC000623062533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062533 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)C2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 8, 8, 12, 11, 16, 16, 16, 16, 8, 8, 23, 23, 23, 23, 23, 8, 3, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062533 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 Building ZINC000623062533 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062533 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 846) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)C2CCCC2)cn1) `ZINC000623062533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062533 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)C2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 9, 9, 13, 12, 16, 16, 16, 16, 7, 7, 23, 23, 23, 23, 23, 7, 3, 13, 13, 13, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 847) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)C2CCCC2)cn1) `ZINC000623062533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062533 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)C2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 8, 8, 12, 11, 16, 16, 16, 16, 8, 8, 23, 23, 23, 23, 23, 8, 3, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062533 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062533 Building ZINC000623062534 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062534 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/848 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C2CCCC2)cn1) `ZINC000623062534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062534 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 9, 14, 14, 14, 14, 7, 7, 16, 16, 16, 16, 16, 7, 2, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/849 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)C2CCCC2)cn1) `ZINC000623062534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062534 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)C2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 9, 17, 17, 17, 17, 6, 6, 16, 16, 16, 16, 16, 6, 2, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062534 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 Building ZINC000623062534 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062534 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 848) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C2CCCC2)cn1) `ZINC000623062534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062534 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 9, 14, 14, 14, 14, 7, 7, 16, 16, 16, 16, 16, 7, 2, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 849) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)C2CCCC2)cn1) `ZINC000623062534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062534 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)C2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 9, 17, 17, 17, 17, 6, 6, 16, 16, 16, 16, 16, 6, 2, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062534 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062534 Building ZINC000623062543 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062543 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/850 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(CN)C2)cn1) `ZINC000623062543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623062543 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(CN)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', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 16, 8, 4, 4, 18, 18, 18, 18, 18, 4, 8, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 8, 8, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/851 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(CN)C2)cn1) `ZINC000623062543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623062543 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(CN)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', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 17, 8, 4, 4, 19, 19, 19, 19, 19, 4, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 8, 8, 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]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062543 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 Building ZINC000623062543 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062543 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 850) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(CN)C2)cn1) `ZINC000623062543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623062543 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(CN)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', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 16, 8, 4, 4, 18, 18, 18, 18, 18, 4, 8, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 8, 8, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 851) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(CN)C2)cn1) `ZINC000623062543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623062543 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(CN)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', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 17, 8, 4, 4, 19, 19, 19, 19, 19, 4, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 8, 8, 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]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062543 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062543 Building ZINC000623062544 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062544 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/852 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(CN)C2)cn1) `ZINC000623062544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623062544 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(CN)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', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 11, 17, 11, 4, 4, 16, 16, 16, 16, 16, 4, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 11, 11, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/853 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(CN)C2)cn1) `ZINC000623062544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623062544 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(CN)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', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 13, 9, 5, 5, 19, 19, 19, 19, 19, 5, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 9, 9, 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]) total number of confs: 98 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062544 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 Building ZINC000623062544 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062544 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 852) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(CN)C2)cn1) `ZINC000623062544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623062544 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(CN)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', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 11, 17, 11, 4, 4, 16, 16, 16, 16, 16, 4, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 11, 11, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 853) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(CN)C2)cn1) `ZINC000623062544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623062544 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(CN)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', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 13, 9, 5, 5, 19, 19, 19, 19, 19, 5, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 9, 9, 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]) total number of confs: 98 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062544 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062544 Building ZINC000623062575 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062575 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/854 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C)CCNCC2)cn1) `ZINC000623062575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062575 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C)CCNCC2)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 3, 3, 8, 8, 8, 8, 8, 3, 2, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/855 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(C)CCNCC2)cn1) `ZINC000623062575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062575 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(C)CCNCC2)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 4, 4, 11, 11, 11, 11, 11, 4, 2, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062575 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 Building ZINC000623062575 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623062575 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 854) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C)CCNCC2)cn1) `ZINC000623062575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623062575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062575 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C)CCNCC2)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 3, 3, 8, 8, 8, 8, 8, 3, 2, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 855) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(C)CCNCC2)cn1) `ZINC000623062575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623062575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623062575 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(C)CCNCC2)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', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 4, 4, 11, 11, 11, 11, 11, 4, 2, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623062575 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623062575 Building ZINC000623063588 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063588 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/856 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@@]3(N)C2)cn1) `ZINC000623063588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063588 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 23, 23, 23, 23, 23, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/857 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@@]3(N)C2)cn1) `ZINC000623063588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063588 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 17, 17, 17, 17, 17, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063588 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 Building ZINC000623063588 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063588 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 856) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@@]3(N)C2)cn1) `ZINC000623063588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063588 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 23, 23, 23, 23, 23, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 857) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@@]3(N)C2)cn1) `ZINC000623063588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063588 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 17, 17, 17, 17, 17, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063588 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063588 Building ZINC000623063589 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063589 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/858 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@]3(N)C2)cn1) `ZINC000623063589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063589 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 16, 16, 16, 16, 16, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/859 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@]3(N)C2)cn1) `ZINC000623063589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063589 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 17, 17, 17, 17, 17, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063589 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 Building ZINC000623063589 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063589 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 858) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@]3(N)C2)cn1) `ZINC000623063589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063589 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 16, 16, 16, 16, 16, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 859) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@]3(N)C2)cn1) `ZINC000623063589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063589 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 17, 17, 17, 17, 17, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063589 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063589 Building ZINC000623063590 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063590 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/860 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@]3(N)C2)cn1) `ZINC000623063590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063590 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 22, 22, 22, 22, 22, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/861 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@]3(N)C2)cn1) `ZINC000623063590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063590 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 20, 20, 20, 20, 20, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063590 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 Building ZINC000623063590 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063590 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 860) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@]3(N)C2)cn1) `ZINC000623063590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063590 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 22, 22, 22, 22, 22, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 861) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@]3(N)C2)cn1) `ZINC000623063590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063590 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC[C@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 20, 20, 20, 20, 20, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063590 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063590 Building ZINC000623063591 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063591 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/862 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@]3(N)C2)cn1) `ZINC000623063591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063591 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 22, 22, 22, 22, 22, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/863 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@]3(N)C2)cn1) `ZINC000623063591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063591 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063591 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 Building ZINC000623063591 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063591 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 862) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@]3(N)C2)cn1) `ZINC000623063591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063591 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 22, 22, 22, 22, 22, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 863) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@]3(N)C2)cn1) `ZINC000623063591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000623063591 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@]3(N)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063591 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063591 Building ZINC000623063922 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063922 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/864 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N)CCC2)cn1) `ZINC000623063922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000623063922 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 18, 21, 21, 21, 21, 6, 6, 17, 17, 17, 17, 17, 6, 2, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/865 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(N)CCC2)cn1) `ZINC000623063922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000623063922 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(N)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 15, 17, 17, 17, 17, 7, 7, 18, 18, 18, 18, 18, 7, 2, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063922 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 Building ZINC000623063922 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063922 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 864) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N)CCC2)cn1) `ZINC000623063922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000623063922 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 18, 21, 21, 21, 21, 6, 6, 17, 17, 17, 17, 17, 6, 2, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 865) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(N)CCC2)cn1) `ZINC000623063922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000623063922 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(N)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 15, 17, 17, 17, 17, 7, 7, 18, 18, 18, 18, 18, 7, 2, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063922 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063922 Building ZINC000623063750 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063750 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/866 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@@H](C)N)C2)cn1) `ZINC000623063750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063750 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 5, 12, 12, 12, 12, 12, 17, 17, 17, 12, 6, 6, 17, 17, 17, 17, 17, 6, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/867 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@@H](C)N)C2)cn1) `ZINC000623063750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063750 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 13, 13, 13, 10, 5, 5, 16, 16, 16, 16, 16, 5, 10, 10, 10, 10, 13, 13, 13, 13, 13, 10, 10, 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]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063750 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 Building ZINC000623063750 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063750 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 866) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@@H](C)N)C2)cn1) `ZINC000623063750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063750 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 5, 12, 12, 12, 12, 12, 17, 17, 17, 12, 6, 6, 17, 17, 17, 17, 17, 6, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 867) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@@H](C)N)C2)cn1) `ZINC000623063750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063750 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 13, 13, 13, 10, 5, 5, 16, 16, 16, 16, 16, 5, 10, 10, 10, 10, 13, 13, 13, 13, 13, 10, 10, 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]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063750 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063750 Building ZINC000623063751 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063751 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/868 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]([C@H](C)N)C2)cn1) `ZINC000623063751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063751 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]([C@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 3, 4, 11, 11, 11, 11, 11, 13, 13, 13, 11, 5, 5, 15, 15, 15, 15, 15, 5, 11, 11, 11, 11, 13, 13, 13, 13, 13, 11, 11, 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]) total number of confs: 77 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/869 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]([C@H](C)N)C2)cn1) `ZINC000623063751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063751 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]([C@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 2, 4, 10, 10, 10, 10, 10, 14, 14, 14, 10, 6, 6, 19, 19, 19, 19, 19, 6, 10, 10, 10, 10, 14, 14, 14, 14, 14, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063751 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 Building ZINC000623063751 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063751 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 868) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]([C@H](C)N)C2)cn1) `ZINC000623063751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063751 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]([C@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 3, 4, 11, 11, 11, 11, 11, 13, 13, 13, 11, 5, 5, 15, 15, 15, 15, 15, 5, 11, 11, 11, 11, 13, 13, 13, 13, 13, 11, 11, 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]) total number of confs: 77 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 869) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]([C@H](C)N)C2)cn1) `ZINC000623063751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063751 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]([C@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 2, 4, 10, 10, 10, 10, 10, 14, 14, 14, 10, 6, 6, 19, 19, 19, 19, 19, 6, 10, 10, 10, 10, 14, 14, 14, 14, 14, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063751 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063751 Building ZINC000623063752 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063752 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/870 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@H](C)N)C2)cn1) `ZINC000623063752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063752 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 15, 15, 15, 15, 15, 5, 9, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 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]) total number of confs: 97 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/871 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@H](C)N)C2)cn1) `ZINC000623063752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063752 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 15, 15, 15, 8, 5, 5, 15, 15, 15, 15, 15, 5, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063752 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 Building ZINC000623063752 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063752 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 870) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@H](C)N)C2)cn1) `ZINC000623063752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063752 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 15, 15, 15, 15, 15, 5, 9, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 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]) total number of confs: 97 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 871) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@H](C)N)C2)cn1) `ZINC000623063752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063752 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]([C@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 15, 15, 15, 8, 5, 5, 15, 15, 15, 15, 15, 5, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063752 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063752 Building ZINC000623063753 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063753 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/872 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]([C@@H](C)N)C2)cn1) `ZINC000623063753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063753 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]([C@@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 14, 14, 14, 14, 14, 5, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 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]) total number of confs: 90 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/873 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]([C@@H](C)N)C2)cn1) `ZINC000623063753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063753 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]([C@@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 14, 14, 14, 14, 14, 5, 9, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 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]) total number of confs: 94 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063753 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 Building ZINC000623063753 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623063753 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 872) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]([C@@H](C)N)C2)cn1) `ZINC000623063753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623063753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063753 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]([C@@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 14, 14, 14, 14, 14, 5, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 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]) total number of confs: 90 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 873) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]([C@@H](C)N)C2)cn1) `ZINC000623063753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623063753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623063753 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]([C@@H](C)N)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', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 14, 14, 14, 14, 14, 5, 9, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 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]) total number of confs: 94 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623063753 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623063753 Building ZINC000623064325 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623064325 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/874 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](CN)CC2)cn1) `ZINC000623064325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623064325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000623064325 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](CN)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 24, 21, 21, 4, 4, 8, 8, 8, 8, 8, 4, 2, 13, 13, 21, 21, 21, 21, 24, 24, 24, 24, 21, 21, 21, 21, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/875 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](CN)CC2)cn1) `ZINC000623064325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623064325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000623064325 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](CN)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 25, 21, 21, 4, 4, 9, 9, 9, 9, 9, 4, 2, 13, 13, 21, 21, 21, 21, 25, 25, 25, 25, 21, 21, 21, 21, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623064325 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 Building ZINC000623064325 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623064325 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 874) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](CN)CC2)cn1) `ZINC000623064325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623064325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000623064325 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](CN)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 24, 21, 21, 4, 4, 8, 8, 8, 8, 8, 4, 2, 13, 13, 21, 21, 21, 21, 24, 24, 24, 24, 21, 21, 21, 21, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 875) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](CN)CC2)cn1) `ZINC000623064325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623064325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000623064325 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](CN)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 25, 21, 21, 4, 4, 9, 9, 9, 9, 9, 4, 2, 13, 13, 21, 21, 21, 21, 25, 25, 25, 25, 21, 21, 21, 21, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623064325 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064325 Building ZINC000623064761 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623064761 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/876 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CNCC3)cn1) `ZINC000623064761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623064761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623064761 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CNCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 11, 17, 17, 17, 17, 7, 7, 20, 20, 20, 20, 20, 7, 2, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/877 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CNCC3)cn1) `ZINC000623064761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623064761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623064761 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CNCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 11, 16, 16, 16, 16, 7, 7, 18, 18, 18, 18, 18, 7, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623064761 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 Building ZINC000623064761 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623064761 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 876) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CNCC3)cn1) `ZINC000623064761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623064761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623064761 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CNCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 11, 17, 17, 17, 17, 7, 7, 20, 20, 20, 20, 20, 7, 2, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 877) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CNCC3)cn1) `ZINC000623064761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623064761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623064761 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CNCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 11, 16, 16, 16, 16, 7, 7, 18, 18, 18, 18, 18, 7, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623064761 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064761 Building ZINC000623064811 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623064811 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/878 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623064811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623064811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623064811 none CCC[C@@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 7, 7, 7, 7, 7, 7, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 22, 6, 17, 17, 17, 17, 17, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 22, 22, 22, 22, 22, 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]) total number of confs: 132 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/879 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623064811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623064811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623064811 none CCC[C@@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 5, 5, 5, 5, 19, 5, 16, 16, 16, 16, 16, 14, 14, 7, 7, 7, 7, 7, 7, 7, 5, 19, 19, 19, 19, 19, 5] 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]) total number of confs: 116 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623064811 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 Building ZINC000623064811 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623064811 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 878) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCC[C@@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623064811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623064811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623064811 none CCC[C@@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 7, 7, 7, 7, 7, 7, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 22, 6, 17, 17, 17, 17, 17, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 22, 22, 22, 22, 22, 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]) total number of confs: 132 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 879) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCC[C@@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623064811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623064811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623064811 none CCC[C@@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 5, 5, 5, 5, 19, 5, 16, 16, 16, 16, 16, 14, 14, 7, 7, 7, 7, 7, 7, 7, 5, 19, 19, 19, 19, 19, 5] 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]) total number of confs: 116 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623064811 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064811 Building ZINC000623064812 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623064812 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/880 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623064812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623064812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623064812 none CCC[C@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 8, 8, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 18, 6, 17, 17, 17, 17, 17, 16, 16, 8, 8, 8, 8, 8, 8, 8, 6, 18, 18, 18, 18, 18, 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]) total number of confs: 110 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/881 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623064812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623064812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623064812 none CCC[C@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 20, 6, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 6, 20, 20, 20, 20, 20, 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]) total number of confs: 119 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623064812 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 Building ZINC000623064812 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623064812 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 880) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCC[C@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623064812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623064812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623064812 none CCC[C@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 8, 8, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 18, 6, 17, 17, 17, 17, 17, 16, 16, 8, 8, 8, 8, 8, 8, 8, 6, 18, 18, 18, 18, 18, 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]) total number of confs: 110 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 881) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCC[C@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623064812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623064812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623064812 none CCC[C@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 20, 6, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 6, 20, 20, 20, 20, 20, 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]) total number of confs: 119 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623064812 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623064812 Building ZINC000623065317 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065317 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/882 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(C)(C)N)cn1) `ZINC000623065317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623065317 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(C)(C)N)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 8, 16, 16, 16, 4, 4, 17, 17, 17, 17, 17, 4, 4, 4, 4, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/883 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(C)(C)N)cn1) `ZINC000623065317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623065317 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(C)(C)N)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 6, 6, 10, 19, 19, 19, 4, 4, 10, 10, 10, 10, 10, 4, 6, 6, 6, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065317 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 Building ZINC000623065317 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065317 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 882) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(C)(C)N)cn1) `ZINC000623065317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623065317 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(C)(C)N)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 8, 16, 16, 16, 4, 4, 17, 17, 17, 17, 17, 4, 4, 4, 4, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 883) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(C)(C)N)cn1) `ZINC000623065317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623065317 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(C)(C)N)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 6, 6, 10, 19, 19, 19, 4, 4, 10, 10, 10, 10, 10, 4, 6, 6, 6, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065317 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065317 Building ZINC000979738914 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000979738914 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/884 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]12) `ZINC000979738914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000979738914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738914 none CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 28, 28, 28, 28, 28, 28, 28, 28, 10, 1, 8, 1, 1, 1, 2, 2, 2, 28, 28, 28, 35, 35, 35, 35, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28] 35 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/885 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]12) `ZINC000979738914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000979738914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738914 none CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 29, 29, 29, 29, 29, 29, 29, 29, 9, 1, 8, 1, 1, 1, 3, 3, 3, 29, 29, 29, 40, 40, 40, 40, 29, 29, 29, 29, 29, 29, 3, 3, 3, 3, 3, 3, 3, 3, 3, 29, 29] 42 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000979738914 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 Building ZINC000979738914 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000979738914 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 884) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]12) `ZINC000979738914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000979738914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738914 none CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 28, 28, 28, 28, 28, 28, 28, 28, 10, 1, 8, 1, 1, 1, 2, 2, 2, 28, 28, 28, 35, 35, 35, 35, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28] 35 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 885) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]12) `ZINC000979738914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000979738914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738914 none CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 29, 29, 29, 29, 29, 29, 29, 29, 9, 1, 8, 1, 1, 1, 3, 3, 3, 29, 29, 29, 40, 40, 40, 40, 29, 29, 29, 29, 29, 29, 3, 3, 3, 3, 3, 3, 3, 3, 3, 29, 29] 42 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000979738914 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738914 Building ZINC000979738917 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000979738917 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/886 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]12) `ZINC000979738917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000979738917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738917 none CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12] 26 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/887 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]12) `ZINC000979738917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000979738917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738917 none CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 9, 9, 9, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9] 24 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000979738917 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 Building ZINC000979738917 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000979738917 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 886) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]12) `ZINC000979738917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000979738917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738917 none CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12] 26 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 887) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]12) `ZINC000979738917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000979738917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738917 none CC(=O)N[C@@H]1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 9, 9, 9, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9] 24 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000979738917 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738917 Building ZINC000979738919 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000979738919 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/888 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000979738919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000979738919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738919 none CC(=O)N[C@@H]1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 29, 29, 29, 8, 1, 20, 1, 1, 1, 1, 1, 1, 29, 29, 29, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/889 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000979738919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000979738919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738919 none CC(=O)N[C@@H]1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 26, 26, 26, 9, 1, 21, 1, 1, 1, 1, 1, 1, 26, 26, 26, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000979738919 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 Building ZINC000979738919 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000979738919 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 888) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(=O)N[C@@H]1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000979738919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000979738919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738919 none CC(=O)N[C@@H]1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 29, 29, 29, 8, 1, 20, 1, 1, 1, 1, 1, 1, 29, 29, 29, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 889) grep: /scratch/xiaobo/170854/xdl-8058088.90/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(=O)N[C@@H]1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC000979738919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000979738919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000979738919 none CC(=O)N[C@@H]1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 26, 26, 26, 9, 1, 21, 1, 1, 1, 1, 1, 1, 26, 26, 26, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000979738919 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000979738919 Building ZINC000623065912 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065912 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/890 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N[C@@H](C)C2)cn1) `ZINC000623065912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065912 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 8, 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, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 7, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 12, 12, 12, 12, 12, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/891 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N[C@@H](C)C2)cn1) `ZINC000623065912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065912 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 8, 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, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065912 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 Building ZINC000623065912 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065912 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 890) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N[C@@H](C)C2)cn1) `ZINC000623065912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065912 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)N[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 8, 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, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 7, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 12, 12, 12, 12, 12, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 891) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N[C@@H](C)C2)cn1) `ZINC000623065912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065912 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)N[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 8, 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, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065912 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065912 Building ZINC000623065913 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065913 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/892 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C)(N)CC2)cn1) `ZINC000623065913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065913 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C)(N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/893 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C)(N)CC2)cn1) `ZINC000623065913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065913 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C)(N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 5, 8, 18, 18, 18, 18, 18, 18, 18, 5, 5, 17, 17, 17, 17, 17, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065913 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 Building ZINC000623065913 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065913 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 892) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C)(N)CC2)cn1) `ZINC000623065913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065913 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C)(N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 893) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C)(N)CC2)cn1) `ZINC000623065913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065913 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C)(N)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 5, 8, 18, 18, 18, 18, 18, 18, 18, 5, 5, 17, 17, 17, 17, 17, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065913 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065913 Building ZINC000623065981 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065981 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/894 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@H](C)C2)cn1) `ZINC000623065981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065981 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 19, 19, 19, 19, 19, 7, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/895 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@H](C)C2)cn1) `ZINC000623065981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065981 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 22, 22, 22, 22, 22, 8, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065981 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 Building ZINC000623065981 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065981 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 894) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@H](C)C2)cn1) `ZINC000623065981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065981 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 19, 19, 19, 19, 19, 7, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 895) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@H](C)C2)cn1) `ZINC000623065981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065981 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 22, 22, 22, 22, 22, 8, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065981 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065981 Building ZINC000623065982 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065982 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/896 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN[C@H](C)C2)cn1) `ZINC000623065982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065982 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 7, 7, 7, 1, 1, 1, 1, 4, 4, 5, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 22, 22, 22, 22, 22, 7, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/897 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN[C@H](C)C2)cn1) `ZINC000623065982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065982 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 31, 31, 31, 31, 31, 10, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10] 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065982 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 Building ZINC000623065982 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065982 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 896) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN[C@H](C)C2)cn1) `ZINC000623065982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065982 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 7, 7, 7, 1, 1, 1, 1, 4, 4, 5, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 22, 22, 22, 22, 22, 7, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 897) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN[C@H](C)C2)cn1) `ZINC000623065982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065982 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 31, 31, 31, 31, 31, 10, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10] 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065982 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065982 Building ZINC000623065983 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065983 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/898 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@@H](C)C2)cn1) `ZINC000623065983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065983 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 25, 25, 25, 25, 25, 10, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/899 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@@H](C)C2)cn1) `ZINC000623065983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065983 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 19, 19, 19, 19, 19, 7, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065983 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 Building ZINC000623065983 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065983 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 898) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@@H](C)C2)cn1) `ZINC000623065983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065983 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 25, 25, 25, 25, 25, 10, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 899) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@@H](C)C2)cn1) `ZINC000623065983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623065983 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 19, 19, 19, 19, 19, 7, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065983 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065983 Building ZINC000674530291 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000674530291 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/900 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000674530291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000674530291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000674530291 none COC[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 11, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 23, 23, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/901 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000674530291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000674530291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000674530291 none COC[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 10, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 25, 25, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 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]) total number of confs: 96 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000674530291 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 Building ZINC000674530291 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000674530291 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 900) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000674530291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000674530291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000674530291 none COC[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 11, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 23, 23, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 901) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: COC[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000674530291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000674530291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000674530291 none COC[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 10, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 25, 25, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 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]) total number of confs: 96 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000674530291 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000674530291 Building ZINC000623065584 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065584 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/902 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCNCC2(C)C)cn1) `ZINC000623065584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623065584 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCNCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 27, 27, 27, 27, 27, 9, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/903 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCNCC2(C)C)cn1) `ZINC000623065584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623065584 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCNCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 20, 20, 20, 20, 20, 7, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065584 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 Building ZINC000623065584 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065584 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 902) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCNCC2(C)C)cn1) `ZINC000623065584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623065584 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCNCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 27, 27, 27, 27, 27, 9, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 903) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCNCC2(C)C)cn1) `ZINC000623065584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623065584 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCNCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 20, 20, 20, 20, 20, 7, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065584 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065584 Building ZINC000623065585 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065585 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/904 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCNCC2(C)C)cn1) `ZINC000623065585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623065585 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCNCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/905 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCNCC2(C)C)cn1) `ZINC000623065585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623065585 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCNCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 24, 24, 24, 24, 24, 7, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/170854/xdl-8058088.90/working/building/ZINC000623065585 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065585 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585 Building ZINC000623065585 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065585 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 904) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCNCC2(C)C)cn1) `ZINC000623065585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623065585 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCNCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 905) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCNCC2(C)C)cn1) `ZINC000623065585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000623065585 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCNCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 24, 24, 24, 24, 24, 7, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/170854/xdl-8058088.90/working/building/ZINC000623065585 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065585 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065585 Building ZINC000623065740 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065740 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/906 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)CCN)cn1) `ZINC000623065740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623065740 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)CCN)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 15, 15, 7, 7, 19, 19, 19, 19, 19, 7, 3, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/907 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)CCN)cn1) `ZINC000623065740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623065740 none CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)CCN)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 15, 15, 6, 6, 15, 15, 15, 15, 15, 6, 4, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065740 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 Building ZINC000623065740 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623065740 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 906) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)CCN)cn1) `ZINC000623065740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623065740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623065740 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)CCN)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 15, 15, 7, 7, 19, 19, 19, 19, 19, 7, 3, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 907) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)CCN)cn1) `ZINC000623065740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623065740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623065740 none CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)CCN)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', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 15, 15, 6, 6, 15, 15, 15, 15, 15, 6, 4, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623065740 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623065740 Building ZINC000353960277 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353960277 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/908 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000353960277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353960277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000353960277 none CCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 25, 27, 31, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 35, 35, 35, 31, 31, 31, 31, 31, 25, 25, 12, 12, 12, 4, 7, 7, 7, 7, 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]) total number of confs: 174 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/909 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000353960277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353960277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000353960277 none CCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 25, 27, 32, 11, 4, 11, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 32, 32, 32, 32, 32, 25, 25, 11, 11, 11, 4, 7, 7, 7, 7, 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]) total number of confs: 183 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000353960277 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 Building ZINC000353960277 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353960277 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 908) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000353960277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353960277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000353960277 none CCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 25, 27, 31, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 35, 35, 35, 31, 31, 31, 31, 31, 25, 25, 12, 12, 12, 4, 7, 7, 7, 7, 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]) total number of confs: 174 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 909) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000353960277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353960277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000353960277 none CCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 25, 27, 32, 11, 4, 11, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 32, 32, 32, 32, 32, 25, 25, 11, 11, 11, 4, 7, 7, 7, 7, 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]) total number of confs: 183 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000353960277 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960277 Building ZINC000353960278 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353960278 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/910 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000353960278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353960278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000353960278 none CCN(CC)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 24, 25, 32, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 32, 32, 32, 32, 32, 24, 24, 12, 12, 12, 4, 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]) total number of confs: 177 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/911 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000353960278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353960278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000353960278 none CCN(CC)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 21, 25, 34, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 34, 34, 34, 34, 34, 21, 21, 12, 12, 12, 4, 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]) total number of confs: 184 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000353960278 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 Building ZINC000353960278 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353960278 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 910) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN(CC)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000353960278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353960278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000353960278 none CCN(CC)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 24, 25, 32, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 32, 32, 32, 32, 32, 24, 24, 12, 12, 12, 4, 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]) total number of confs: 177 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 911) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN(CC)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000353960278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353960278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000353960278 none CCN(CC)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 21, 25, 34, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 34, 34, 34, 34, 34, 21, 21, 12, 12, 12, 4, 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]) total number of confs: 184 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000353960278 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000353960278 Building ZINC000408222161 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408222161 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/912 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 7, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/913 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 8, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/914 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/914' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 7, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/915 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/915' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 8, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408222161 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 Building ZINC000408222161 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408222161 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 912) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 7, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 913) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 8, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 914) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 7, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 915) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 8, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408222161 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 Building ZINC000408222161 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408222161 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 912) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 7, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 913) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 8, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 914) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 7, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 915) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 8, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408222161 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 Building ZINC000408222161 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408222161 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 912) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 7, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 913) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 8, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 914) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 7, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 915) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1) `ZINC000408222161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408222161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000408222161 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCCN3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 8, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408222161 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408222161 Building ZINC000162608867 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000162608867 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/916 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H]1CC(=O)NC1=O) `ZINC000162608867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000162608867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000162608867 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 13, 27, 27, 27, 27, 27, 27, 27, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27] 34 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]) total number of confs: 138 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/917 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H]1CC(=O)NC1=O) `ZINC000162608867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000162608867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000162608867 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 42, 42, 42, 42, 42, 42, 42, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 42, 42, 42] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000162608867 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 Building ZINC000162608867 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000162608867 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 916) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H]1CC(=O)NC1=O) `ZINC000162608867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000162608867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000162608867 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 13, 27, 27, 27, 27, 27, 27, 27, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27] 34 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]) total number of confs: 138 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 917) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H]1CC(=O)NC1=O) `ZINC000162608867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000162608867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000162608867 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 42, 42, 42, 42, 42, 42, 42, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 42, 42, 42] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000162608867 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162608867 Building ZINC000162609003 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000162609003 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/918 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CC(=O)NC1=O) `ZINC000162609003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000162609003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000162609003 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 41, 41, 41] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/919 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CC(=O)NC1=O) `ZINC000162609003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000162609003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000162609003 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 28, 28, 28, 28, 28, 28, 28, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 28, 28, 28] 35 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]) total number of confs: 141 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000162609003 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 Building ZINC000162609003 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000162609003 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 918) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CC(=O)NC1=O) `ZINC000162609003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000162609003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000162609003 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 41, 41, 41] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 919) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CC(=O)NC1=O) `ZINC000162609003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000162609003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000162609003 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 28, 28, 28, 28, 28, 28, 28, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 28, 28, 28] 35 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]) total number of confs: 141 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000162609003 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000162609003 Building ZINC000408224076 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224076 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/920 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/921 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/922 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/922' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/923 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/923' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224076 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 Building ZINC000408224076 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224076 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 920) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 921) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 922) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 923) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224076 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 Building ZINC000408224076 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224076 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 920) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 921) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 922) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 923) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224076 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 Building ZINC000408224076 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224076 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 920) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 921) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 922) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 923) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224076 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224076 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224076 Building ZINC000408224077 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224077 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/924 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/925 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/926 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/926' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/927 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/927' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224077 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 Building ZINC000408224077 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224077 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 924) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 925) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 926) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 927) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224077 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 Building ZINC000408224077 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224077 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 924) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 925) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 926) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 927) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224077 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 Building ZINC000408224077 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224077 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 924) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 925) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 926) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 927) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224077.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224077 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224077 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224077 Building ZINC000408224080 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224080 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/928 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/929 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/930 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/930' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/931 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/931' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224080 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 Building ZINC000408224080 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224080 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 928) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 929) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 930) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 931) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224080 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 Building ZINC000408224080 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224080 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 928) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 929) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 930) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 931) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224080 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 Building ZINC000408224080 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224080 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 928) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 929) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 930) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 931) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224080 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224080 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224080 Building ZINC000408224082 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224082 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/932 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 30, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/933 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 30, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/934 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/934' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 27, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/935 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/935' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 27, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224082 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 Building ZINC000408224082 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224082 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 932) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 30, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 933) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 30, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 934) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 27, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 935) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 27, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224082 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 Building ZINC000408224082 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224082 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 932) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 30, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 933) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 30, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 934) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 27, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 935) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 27, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224082 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 Building ZINC000408224082 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408224082 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 932) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 30, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 933) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 30, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 934) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 27, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 935) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C) `ZINC000408224082.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408224082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000408224082 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 10, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 27, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224082 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224082 Building ZINC000623066481 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623066481 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/936 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](CN)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623066481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623066481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066481 none CCCC[C@H](CN)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens 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, 14, 11, 7, 2, 7, 7, 9, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 19, 6, 14, 14, 14, 14, 14, 14, 13, 13, 13, 9, 9, 9, 9, 2, 6, 19, 19, 19, 19, 19, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/937 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](CN)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623066481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623066481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066481 none CCCC[C@H](CN)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens 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, 17, 15, 8, 2, 8, 8, 12, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 2, 6, 14, 14, 14, 14, 14, 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623066481 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 Building ZINC000623066481 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623066481 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 936) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCC[C@H](CN)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623066481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623066481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066481 none CCCC[C@H](CN)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens 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, 14, 11, 7, 2, 7, 7, 9, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 19, 6, 14, 14, 14, 14, 14, 14, 13, 13, 13, 9, 9, 9, 9, 2, 6, 19, 19, 19, 19, 19, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 937) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCC[C@H](CN)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623066481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623066481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066481 none CCCC[C@H](CN)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens 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, 17, 15, 8, 2, 8, 8, 12, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 2, 6, 14, 14, 14, 14, 14, 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623066481 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066481 Building ZINC000623066482 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623066482 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/938 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](CN)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623066482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623066482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066482 none CCCC[C@@H](CN)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 11, 7, 2, 7, 7, 9, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 18, 6, 19, 19, 19, 19, 19, 13, 13, 11, 11, 9, 9, 9, 9, 2, 6, 18, 18, 18, 18, 18, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/939 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](CN)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623066482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623066482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066482 none CCCC[C@@H](CN)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens 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, 13, 7, 2, 7, 7, 8, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 6, 18, 18, 18, 18, 18, 14, 14, 13, 13, 8, 8, 8, 8, 2, 6, 16, 16, 16, 16, 16, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623066482 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 Building ZINC000623066482 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623066482 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 938) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCC[C@@H](CN)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623066482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623066482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066482 none CCCC[C@@H](CN)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 11, 7, 2, 7, 7, 9, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 18, 6, 19, 19, 19, 19, 19, 13, 13, 11, 11, 9, 9, 9, 9, 2, 6, 18, 18, 18, 18, 18, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 939) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCCC[C@@H](CN)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000623066482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623066482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066482 none CCCC[C@@H](CN)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens 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, 13, 7, 2, 7, 7, 8, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 6, 18, 18, 18, 18, 18, 14, 14, 13, 13, 8, 8, 8, 8, 2, 6, 16, 16, 16, 16, 16, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623066482 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066482 Building ZINC000623066834 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623066834 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/940 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(C)(C)CN)cn1) `ZINC000623066834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623066834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066834 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(C)(C)CN)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', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 5, 14, 14, 14, 17, 4, 4, 16, 16, 16, 16, 16, 4, 4, 4, 4, 5, 5, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 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]) total number of confs: 123 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/941 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(C)(C)CN)cn1) `ZINC000623066834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623066834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066834 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(C)(C)CN)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', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 3, 15, 15, 15, 19, 4, 4, 15, 15, 15, 15, 15, 4, 2, 2, 2, 3, 3, 15, 15, 15, 15, 15, 15, 19, 19, 19, 19, 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]) total number of confs: 129 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623066834 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 Building ZINC000623066834 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623066834 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 940) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(C)(C)CN)cn1) `ZINC000623066834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623066834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066834 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(C)(C)CN)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', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 5, 14, 14, 14, 17, 4, 4, 16, 16, 16, 16, 16, 4, 4, 4, 4, 5, 5, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 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]) total number of confs: 123 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 941) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(C)(C)CN)cn1) `ZINC000623066834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623066834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000623066834 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(C)(C)CN)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', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 3, 15, 15, 15, 19, 4, 4, 15, 15, 15, 15, 15, 4, 2, 2, 2, 3, 3, 15, 15, 15, 15, 15, 15, 19, 19, 19, 19, 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]) total number of confs: 129 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623066834 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623066834 Building ZINC000408224731 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408224731 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/942 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C)(CO)CC2)cn1) `ZINC000408224731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000408224731 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C)(CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 5, 6, 15, 15, 15, 15, 15, 30, 15, 15, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 30, 30, 90, 15, 15, 15, 15, 6] 150 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 194 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/943 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C)(CO)CC2)cn1) `ZINC000408224731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000408224731 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C)(CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 5, 6, 15, 15, 15, 15, 15, 28, 15, 15, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 28, 28, 84, 15, 15, 15, 15, 6] 150 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 187 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224731 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 Building ZINC000408224731 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408224731 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 942) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C)(CO)CC2)cn1) `ZINC000408224731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408224731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000408224731 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C)(CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 5, 6, 15, 15, 15, 15, 15, 30, 15, 15, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 30, 30, 90, 15, 15, 15, 15, 6] 150 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 194 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 943) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C)(CO)CC2)cn1) `ZINC000408224731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408224731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000408224731 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C)(CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 5, 6, 15, 15, 15, 15, 15, 28, 15, 15, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 28, 28, 84, 15, 15, 15, 15, 6] 150 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 187 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408224731 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408224731 Building ZINC000408226145 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226145 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/944 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/944' -> `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]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/945 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/945' -> `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]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/946 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/946' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/947 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/947' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226145 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 Building ZINC000408226145 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226145 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 944) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 945) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 946) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 947) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226145 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 Building ZINC000408226145 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226145 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 944) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 945) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 946) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 947) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226145 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 Building ZINC000408226145 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226145 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 944) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 945) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 946) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 947) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226145.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226145 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226145 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226145 Building ZINC000408226147 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226147 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/948 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/948' -> `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]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/949 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/949' -> `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]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/950 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/950' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/951 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/951' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226147 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 Building ZINC000408226147 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226147 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 948) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 949) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 950) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 951) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226147 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 Building ZINC000408226147 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226147 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 948) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 949) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 950) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 951) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226147 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 Building ZINC000408226147 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226147 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 948) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 949) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 950) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 951) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226147.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226147 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226147 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226147 Building ZINC000408226149 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226149 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/952 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/952' -> `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]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 21, 39, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/953 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/953' -> `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]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 40, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/954 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/954' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 21, 39, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/955 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/955' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 40, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226149 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 Building ZINC000408226149 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226149 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 952) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 21, 39, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 953) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 40, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 954) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 21, 39, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 955) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 40, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226149 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 Building ZINC000408226149 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226149 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 952) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 21, 39, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 953) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 40, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 954) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 21, 39, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 955) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 40, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226149 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 Building ZINC000408226149 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226149 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 952) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 21, 39, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 953) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 40, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 954) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 21, 39, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 955) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@@H](C)C1) `ZINC000408226149.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226149 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 40, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226149 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226149 Building ZINC000408226150 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226150 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/956 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/956' -> `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]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/957 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/957' -> `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]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/958 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/958' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/959 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/959' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226150 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 Building ZINC000408226150 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226150 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 956) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 957) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 958) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 959) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226150 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 Building ZINC000408226150 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226150 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 956) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 957) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 958) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 959) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226150 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 Building ZINC000408226150 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000408226150 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 956) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 957) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `2' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 2 (index: 958) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 46, 46, 46, 46, 46, 46, 46, 46, 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, 44]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `3' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 3 (index: 959) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCN(C)[C@H](C)C1) `ZINC000408226150.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000408226150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000408226150 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000408226150 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/1.* 2: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/2.* 3: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/3.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000408226150 Building ZINC000623067643 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067643 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/960 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@@H]3C2)cn1) `ZINC000623067643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067643 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 14, 14, 14, 14, 14, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/961 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@@H]3C2)cn1) `ZINC000623067643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067643 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 15, 15, 15, 15, 15, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067643 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 Building ZINC000623067643 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067643 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 960) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@@H]3C2)cn1) `ZINC000623067643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067643 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 14, 14, 14, 14, 14, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 961) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@@H]3C2)cn1) `ZINC000623067643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067643 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 15, 15, 15, 15, 15, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067643 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067643 Building ZINC000623067644 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067644 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/962 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1) `ZINC000623067644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067644 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 5, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 21, 21, 21, 21, 21, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/170854/xdl-8058088.90/working/building/ZINC000623067644 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/963 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1) `ZINC000623067644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067644 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 4, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067644 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644 Building ZINC000623067644 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067644 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 962) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1) `ZINC000623067644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067644 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 5, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 21, 21, 21, 21, 21, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/170854/xdl-8058088.90/working/building/ZINC000623067644 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 963) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1) `ZINC000623067644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067644 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 8, 8, 1, 1, 1, 1, 4, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067644 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067644 Building ZINC000623067645 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067645 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/964 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@@H]3C2)cn1) `ZINC000623067645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067645 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 21, 21, 21, 21, 21, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/965 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@@H]3C2)cn1) `ZINC000623067645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067645 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 19, 19, 19, 19, 19, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067645 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 Building ZINC000623067645 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067645 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 964) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@@H]3C2)cn1) `ZINC000623067645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067645 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 21, 21, 21, 21, 21, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 965) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@@H]3C2)cn1) `ZINC000623067645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067645 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 19, 19, 19, 19, 19, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067645 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067645 Building ZINC000623067646 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067646 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/966 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@H]3C2)cn1) `ZINC000623067646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067646 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/967 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@H]3C2)cn1) `ZINC000623067646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067646 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 4, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 22, 22, 22, 22, 22, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067646 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 Building ZINC000623067646 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067646 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 966) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@H]3C2)cn1) `ZINC000623067646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067646 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 967) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@H]3C2)cn1) `ZINC000623067646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623067646 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 4, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 22, 22, 22, 22, 22, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067646 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067646 Building ZINC000623067975 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067975 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/968 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H]1CCC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@@H]21) `ZINC000623067975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067975 none N[C@@H]1CCC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 20, 20] 40 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]) total number of confs: 41 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/969 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H]1CCC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@@H]21) `ZINC000623067975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067975 none N[C@@H]1CCC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 18, 18] 39 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067975 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 Building ZINC000623067975 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067975 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 968) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: N[C@@H]1CCC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@@H]21) `ZINC000623067975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067975 none N[C@@H]1CCC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 20, 20] 40 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]) total number of confs: 41 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 969) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: N[C@@H]1CCC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@@H]21) `ZINC000623067975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067975 none N[C@@H]1CCC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 18, 18] 39 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067975 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067975 Building ZINC000623067976 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067976 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/970 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H]1CCC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21) `ZINC000623067976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067976 none N[C@@H]1CCC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 9, 21, 21] 42 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/971 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H]1CCC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21) `ZINC000623067976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067976 none N[C@@H]1CCC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 19, 19] 39 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]) total number of confs: 40 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067976 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 Building ZINC000623067976 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067976 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 970) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: N[C@@H]1CCC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21) `ZINC000623067976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067976 none N[C@@H]1CCC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 9, 21, 21] 42 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 971) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: N[C@@H]1CCC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21) `ZINC000623067976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067976 none N[C@@H]1CCC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 19, 19] 39 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]) total number of confs: 40 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067976 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067976 Building ZINC000623067977 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067977 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/972 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H]1CCC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21) `ZINC000623067977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067977 none N[C@@H]1CCC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/973 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H]1CCC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21) `ZINC000623067977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067977 none N[C@@H]1CCC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 29, 29, 29, 29, 29, 8, 1, 14, 1, 1, 1, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 29, 29] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067977 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 Building ZINC000623067977 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067977 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 972) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: N[C@@H]1CCC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21) `ZINC000623067977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067977 none N[C@@H]1CCC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 973) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: N[C@@H]1CCC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21) `ZINC000623067977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000623067977 none N[C@@H]1CCC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 29, 29, 29, 29, 29, 8, 1, 14, 1, 1, 1, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 29, 29] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067977 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067977 Building ZINC000623067927 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067927 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/974 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@H]2CNC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067927 none O=C(N[C@@H]1CC[C@H]2CNC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 10, 10, 10, 10, 10, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/975 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@H]2CNC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067927 none O=C(N[C@@H]1CC[C@H]2CNC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 1, 1, 10, 10, 10, 10, 10, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067927 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 Building ZINC000623067927 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067927 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 974) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC[C@H]2CNC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067927 none O=C(N[C@@H]1CC[C@H]2CNC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 10, 10, 10, 10, 10, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 975) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC[C@H]2CNC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067927 none O=C(N[C@@H]1CC[C@H]2CNC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 1, 1, 10, 10, 10, 10, 10, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067927 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067927 Building ZINC000623067928 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067928 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/976 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CNC[C@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067928 none O=C(N[C@@H]1CC[C@@H]2CNC[C@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 12, 12, 12, 12, 12, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/977 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CNC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067928 none O=C(N[C@@H]1CC[C@@H]2CNC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067928 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 Building ZINC000623067928 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067928 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 976) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC[C@@H]2CNC[C@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067928 none O=C(N[C@@H]1CC[C@@H]2CNC[C@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 12, 12, 12, 12, 12, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 977) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC[C@@H]2CNC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067928 none O=C(N[C@@H]1CC[C@@H]2CNC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067928 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067928 Building ZINC000623067929 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067929 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/978 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@H]2CNC[C@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067929 none O=C(N[C@@H]1CC[C@H]2CNC[C@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 11, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 9, 9, 9, 9, 9, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/979 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@H]2CNC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067929 none O=C(N[C@@H]1CC[C@H]2CNC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 9, 9, 9, 9, 9, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067929 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 Building ZINC000623067929 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067929 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 978) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@H]2CNC[C@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067929 none O=C(N[C@@H]1CC[C@H]2CNC[C@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 11, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 9, 9, 9, 9, 9, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 979) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@H]2CNC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067929 none O=C(N[C@@H]1CC[C@H]2CNC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 9, 9, 9, 9, 9, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067929 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067929 Building ZINC000623067930 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067930 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/980 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CNC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067930 none O=C(N[C@@H]1CC[C@@H]2CNC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 11, 11, 11, 11, 11, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/981 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CNC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067930 none O=C(N[C@@H]1CC[C@@H]2CNC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067930 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 Building ZINC000623067930 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623067930 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 980) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC[C@@H]2CNC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623067930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067930 none O=C(N[C@@H]1CC[C@@H]2CNC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 11, 11, 11, 11, 11, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 981) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: O=C(N[C@@H]1CC[C@@H]2CNC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000623067930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623067930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623067930 none O=C(N[C@@H]1CC[C@@H]2CNC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 10, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623067930 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623067930 Building ZINC000623068000 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068000 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/982 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@H]2C)cn1) `ZINC000623068000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068000 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 15, 7, 7, 7, 7, 6, 6, 19, 19, 19, 19, 19, 6, 7, 7, 15, 15, 15, 15, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/983 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@H]2C)cn1) `ZINC000623068000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068000 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 20, 9, 9, 9, 9, 4, 4, 23, 23, 23, 23, 23, 4, 9, 9, 20, 20, 20, 20, 9, 9, 9, 9, 9, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068000 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 Building ZINC000623068000 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068000 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 982) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@H]2C)cn1) `ZINC000623068000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068000 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 15, 7, 7, 7, 7, 6, 6, 19, 19, 19, 19, 19, 6, 7, 7, 15, 15, 15, 15, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 983) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@H]2C)cn1) `ZINC000623068000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068000 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 20, 9, 9, 9, 9, 4, 4, 23, 23, 23, 23, 23, 4, 9, 9, 20, 20, 20, 20, 9, 9, 9, 9, 9, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068000 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068000 Building ZINC000623068001 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068001 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/984 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@@H]2C)cn1) `ZINC000623068001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068001 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 19, 9, 9, 9, 9, 4, 4, 27, 27, 27, 27, 27, 4, 9, 9, 19, 19, 19, 19, 9, 9, 9, 9, 9, 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]) total number of confs: 147 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/985 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@@H]2C)cn1) `ZINC000623068001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068001 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 19, 9, 9, 9, 9, 6, 6, 22, 22, 22, 22, 22, 6, 9, 9, 19, 19, 19, 19, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068001 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 Building ZINC000623068001 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068001 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 984) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@@H]2C)cn1) `ZINC000623068001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068001 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 19, 9, 9, 9, 9, 4, 4, 27, 27, 27, 27, 27, 4, 9, 9, 19, 19, 19, 19, 9, 9, 9, 9, 9, 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]) total number of confs: 147 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 985) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@@H]2C)cn1) `ZINC000623068001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068001 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 19, 9, 9, 9, 9, 6, 6, 22, 22, 22, 22, 22, 6, 9, 9, 19, 19, 19, 19, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068001 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068001 Building ZINC000623068002 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068002 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/986 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@@H]2C)cn1) `ZINC000623068002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068002 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 18, 8, 8, 8, 8, 4, 4, 21, 21, 21, 21, 21, 4, 8, 8, 18, 18, 18, 18, 8, 8, 8, 8, 8, 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]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/987 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@@H]2C)cn1) `ZINC000623068002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068002 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 15, 7, 7, 7, 7, 6, 6, 21, 21, 21, 21, 21, 6, 7, 7, 15, 15, 15, 15, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068002 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 Building ZINC000623068002 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068002 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 986) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@@H]2C)cn1) `ZINC000623068002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068002 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 18, 8, 8, 8, 8, 4, 4, 21, 21, 21, 21, 21, 4, 8, 8, 18, 18, 18, 18, 8, 8, 8, 8, 8, 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]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 987) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@@H]2C)cn1) `ZINC000623068002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068002 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CN)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 15, 7, 7, 7, 7, 6, 6, 21, 21, 21, 21, 21, 6, 7, 7, 15, 15, 15, 15, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068002 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068002 Building ZINC000623068003 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068003 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/988 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@H]2C)cn1) `ZINC000623068003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068003 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 17, 7, 7, 7, 7, 6, 6, 22, 22, 22, 22, 22, 6, 7, 7, 17, 17, 17, 17, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/989 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@H]2C)cn1) `ZINC000623068003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068003 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 17, 9, 9, 9, 9, 4, 4, 23, 23, 23, 23, 23, 4, 9, 9, 17, 17, 17, 17, 9, 9, 9, 9, 9, 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]) total number of confs: 129 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068003 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 Building ZINC000623068003 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068003 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 988) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@H]2C)cn1) `ZINC000623068003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068003 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 17, 7, 7, 7, 7, 6, 6, 22, 22, 22, 22, 22, 6, 7, 7, 17, 17, 17, 17, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 989) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@H]2C)cn1) `ZINC000623068003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068003 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CN)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 17, 9, 9, 9, 9, 4, 4, 23, 23, 23, 23, 23, 4, 9, 9, 17, 17, 17, 17, 9, 9, 9, 9, 9, 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]) total number of confs: 129 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068003 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068003 Building ZINC000623068103 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068103 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/990 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCN)cn1) `ZINC000623068103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623068103 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 12, 12, 16, 6, 6, 16, 16, 16, 16, 16, 6, 2, 6, 6, 6, 12, 12, 12, 12, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/991 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)CCCN)cn1) `ZINC000623068103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623068103 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)CCCN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 13, 13, 16, 6, 6, 16, 16, 16, 16, 16, 6, 2, 6, 6, 6, 13, 13, 13, 13, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068103 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 Building ZINC000623068103 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068103 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 990) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCN)cn1) `ZINC000623068103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623068103 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 12, 12, 16, 6, 6, 16, 16, 16, 16, 16, 6, 2, 6, 6, 6, 12, 12, 12, 12, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 991) grep: /scratch/xiaobo/170854/xdl-8058088.90/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)CCCN)cn1) `ZINC000623068103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623068103 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)CCCN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 13, 13, 16, 6, 6, 16, 16, 16, 16, 16, 6, 2, 6, 6, 6, 13, 13, 13, 13, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068103 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068103 Building ZINC000623068104 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068104 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/992 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCN)cn1) `ZINC000623068104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623068104 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 11, 16, 19, 5, 5, 15, 15, 15, 15, 15, 5, 2, 6, 6, 6, 13, 13, 16, 14, 19, 19, 19, 19, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/993 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCN)cn1) `ZINC000623068104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623068104 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 13, 17, 21, 6, 6, 17, 17, 17, 17, 17, 6, 2, 6, 6, 6, 14, 14, 17, 16, 21, 21, 21, 21, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068104 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 Building ZINC000623068104 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068104 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 992) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCN)cn1) `ZINC000623068104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623068104 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 11, 16, 19, 5, 5, 15, 15, 15, 15, 15, 5, 2, 6, 6, 6, 13, 13, 16, 14, 19, 19, 19, 19, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 993) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCN)cn1) `ZINC000623068104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000623068104 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCN)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 13, 17, 21, 6, 6, 17, 17, 17, 17, 17, 6, 2, 6, 6, 6, 14, 14, 17, 16, 21, 21, 21, 21, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068104 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068104 Building ZINC000623068179 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068179 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/994 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@H]3C2)cn1) `ZINC000623068179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623068179 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 6, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/995 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@H]3C2)cn1) `ZINC000623068179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623068179 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 18, 18, 18, 18, 18, 6, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068179 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 Building ZINC000623068179 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068179 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 994) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@H]3C2)cn1) `ZINC000623068179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623068179 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 6, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 995) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@H]3C2)cn1) `ZINC000623068179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623068179 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 18, 18, 18, 18, 18, 6, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068179 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068179 Building ZINC000623068180 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068180 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/996 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@@H]3C2)cn1) `ZINC000623068180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623068180 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 21, 21, 21, 21, 21, 7, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/997 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@@H]3C2)cn1) `ZINC000623068180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623068180 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 18, 18, 18, 18, 18, 7, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068180 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 Building ZINC000623068180 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068180 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 996) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@@H]3C2)cn1) `ZINC000623068180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623068180 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 21, 21, 21, 21, 21, 7, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 997) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@@H]3C2)cn1) `ZINC000623068180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000623068180 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CNC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 18, 18, 18, 18, 18, 7, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068180 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068180 Building ZINC000623068195 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068195 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/998 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](CN)C2CC2)cn1) `ZINC000623068195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068195 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 3, 3, 4, 4, 6, 6, 14, 6, 12, 12, 4, 4, 20, 20, 20, 20, 20, 4, 4, 4, 4, 14, 14, 14, 14, 12, 12, 12, 12, 12, 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]) total number of confs: 144 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/999 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](CN)C2CC2)cn1) `ZINC000623068195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068195 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 3, 3, 4, 4, 7, 7, 13, 7, 12, 12, 5, 5, 23, 23, 23, 23, 23, 5, 4, 4, 4, 13, 13, 13, 13, 12, 12, 12, 12, 12, 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]) total number of confs: 147 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068195 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 Building ZINC000623068195 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623068195 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 998) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](CN)C2CC2)cn1) `ZINC000623068195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068195 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 3, 3, 4, 4, 6, 6, 14, 6, 12, 12, 4, 4, 20, 20, 20, 20, 20, 4, 4, 4, 4, 14, 14, 14, 14, 12, 12, 12, 12, 12, 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]) total number of confs: 144 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 mkdir: created directory `1' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/1 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 1 (index: 999) grep: /scratch/xiaobo/170854/xdl-8058088.90/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](CN)C2CC2)cn1) `ZINC000623068195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623068195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068195 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 3, 3, 4, 4, 7, 7, 13, 7, 12, 12, 5, 5, 23, 23, 23, 23, 23, 5, 4, 4, 4, 13, 13, 13, 13, 12, 12, 12, 12, 12, 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]) total number of confs: 147 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068195 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 1: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/1.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068195 Building ZINC000623068196 mkdir: created directory `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068196' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068196 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000623068196 mkdir: created directory `0' /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068196/0 /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068196 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/170854/xdl-8058088.90/working/3D/1000 `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](CN)C2CC2)cn1) `ZINC000623068196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623068196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000623068196 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](CN)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 4, 4, 8, 8, 15, 8, 14, 14, 6, 6, 21, 21, 21, 21, 21, 6, 4, 4, 4, 15, 15, 15, 15, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 146 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068196 /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Finished preparing ZINC000623068196 Recording results /scratch/xiaobo/170854/xdl-8058088.90/working /scratch/xiaobo/170854/xdl-8058088.90 Appending to /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.* 0: /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068196/0.* Removing working files in /scratch/xiaobo/170854/xdl-8058088.90/working/building/ZINC000623068196 /scratch/xiaobo/170854/xdl-8058088.90 Compressing combined databse files /scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/170854/xdl-8058088.90/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/170854/xdl-8058088.90/working/3D/1001' removed directory: `/scratch/xiaobo/170854/xdl-8058088.90/working/3D' rmdir: removing directory, `/scratch/xiaobo/170854/xdl-8058088.90/working/building' rmdir: removing directory, `/scratch/xiaobo/170854/xdl-8058088.90/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/170854/xdl-8058088.90' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xdl' `/scratch/xiaobo/170854/xdl-8058088.90/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xdl/finished' `/scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xdl/finished/xdl.db2.gz' removed `/scratch/xiaobo/170854/xdl-8058088.90/finished/xdl.db2.gz' removed directory: `/scratch/xiaobo/170854/xdl-8058088.90/finished' removed directory: `/scratch/xiaobo/170854/xdl-8058088.90'